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diff --git a/cmml/18-0008_Eva_Maleckova/GC-MS/181204_DoubleChecked/.Rhistory b/cmml/18-0008_Eva_Maleckova/GC-MS/181204_DoubleChecked/.Rhistory
deleted file mode 100755
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--- a/cmml/18-0008_Eva_Maleckova/GC-MS/181204_DoubleChecked/.Rhistory
+++ /dev/null
@@ -1,167 +0,0 @@
-rm(list = ls())
-### Mac dir tree or ### PC dir tree
-if(dir.exists('/Volumes/data/')){setwd('/Volumes/data/')}; if(dir.exists('M:/MSlab/')){setwd('M:/')}
-source('MSlab/17_Dominik_Brilhaus/00_CustomR_Functions/01_MSLab.R')
-wd <- 'MSlab/05_projects/18-0008_Eva_Maleckova/GC-MS/'
-setwd(wd)
-required.packages <- c("Rmisc", "plyr", "ggplot2", "reshape2", "gridExtra", 'openxlsx')
-for(package in required.packages)
-{
-print(package)
-## Check if package is installed. If not, install
-if(!package %in% row.names(installed.packages())){install.packages(package, repos ="https://cran.uni-muenster.de/")}
-# ## Check if package is up to date. If not, update
-# update.packages(package, repos = "https://cran.uni-muenster.de/")
-## Load package
-library(package, character.only = T)
-}
-theme_dominik <-
-theme(panel.grid = element_blank(), panel.background = element_blank(), panel.border = element_rect(fill = NA)) +
-theme(axis.text = element_text(color = "black"), axis.ticks = element_line(color = "black"), axis.title = element_text(color = "black")) +
-theme(plot.title = element_text(face= "bold")) +
-theme(aspect.ratio = 1) +
-theme(strip.background = element_blank(), strip.text = element_text(size = 10, face = "bold")) +
-theme(legend.position = "right", legend.title = element_blank()) #legend.direction = "vertical",
-nice.date <- format(Sys.time(), "%y%m%d")
-report.xlsx <- dir(pattern = 'QuantReport')
-report.xlsx <- grep('xlsx', value = T, report.xlsx)
-report.xlsx
-rm(list = ls())
-### Mac dir tree or ### PC dir tree
-if(dir.exists('/Volumes/data/')){setwd('/Volumes/data/')}; if(dir.exists('M:/MSlab/')){setwd('M:/')}
-source('MSlab/17_Dominik_Brilhaus/00_CustomR_Functions/01_MSLab.R')
-wd <- 'MSlab/05_projects/18-0008_Eva_Maleckova/GC-MS/181204_DoubleChecked/'
-setwd(wd)
-#################################################
-required.packages <- c("Rmisc", "plyr", "ggplot2", "reshape2", "gridExtra", 'openxlsx')
-for(package in required.packages)
-{
-print(package)
-## Check if package is installed. If not, install
-if(!package %in% row.names(installed.packages())){install.packages(package, repos ="https://cran.uni-muenster.de/")}
-# ## Check if package is up to date. If not, update
-# update.packages(package, repos = "https://cran.uni-muenster.de/")
-## Load package
-library(package, character.only = T)
-}
-theme_dominik <-
-theme(panel.grid = element_blank(), panel.background = element_blank(), panel.border = element_rect(fill = NA)) +
-theme(axis.text = element_text(color = "black"), axis.ticks = element_line(color = "black"), axis.title = element_text(color = "black")) +
-theme(plot.title = element_text(face= "bold")) +
-theme(aspect.ratio = 1) +
-theme(strip.background = element_blank(), strip.text = element_text(size = 10, face = "bold")) +
-theme(legend.position = "right", legend.title = element_blank()) #legend.direction = "vertical",
-nice.date <- format(Sys.time(), "%y%m%d")
-#################################################
-### Identify quant report
-report.xlsx <- dir(pattern = 'QuantReport')
-report.xlsx <- grep('xlsx', value = T, report.xlsx)
-collect.reports <- list()
-pdf(paste(nice.date, "QC_QuantReport.pdf", sep = '_'), width = 15, height = 15)
-for(report.name in report.xlsx)
-{
-## Load QuantReport book
-GC.report <- read.xlsx(report.name, "Summary")
-clean.report <- report.extract(GC.report)
-clean.report$data.source <- report.name
-colnames(clean.report) <- gsub(' ', '.', colnames(clean.report))
-### Rename compounds
-clean.report$Compound <- gsub("Gaba", "GABA", clean.report$Compound)
-clean.report$Compound <- gsub("a ", "alpha-", clean.report$Compound)
-clean.report$Compound <- gsub("b ", "beta-", clean.report$Compound)
-clean.report$Compound <- gsub("ic Acid", "ate", clean.report$Compound)
-clean.report$Compound <- gsub(" 2TMS", "", clean.report$Compound)
-# clean.report$Compound <- gsub(" 3TMS", "", clean.report$Compound)
-clean.report[!grepl("alpha-", clean.report$Compound) & !grepl("beta-", clean.report$Compound), "Compound"] <- paste("'", clean.report[!grepl("alpha-", clean.report$Compound) & !grepl("beta-", clean.report$Compound), "Compound"], "'", sep = "")
-colnames(clean.report) <- gsub(" ", ".", colnames(clean.report))
-#### Distinguish between split and splitless
-#### and keep only those compounds that passed the manual qc
-split.df <- data.frame(Acq.Method.File = unique(clean.report$Acq.Method.File))
-split.df[grepl("split", unique(split.df$Acq.Method.File), ignore.case = T) & !grepl("splitles", unique(split.df$Acq.Method.File), ignore.case = T), "Acq.Method.Condensed"] <- "split"
-split.df[grepl("splitles", unique(split.df$Acq.Method.File), ignore.case = T), "Acq.Method.Condensed"] <- "splitless"
-###
-warning("Double-check correct assignment of split / splitless")
-print(split.df)
-clean.report <- merge(clean.report, split.df, "Acq.Method.File")
-unique(clean.report[, c('Sample.Type','Sample.Name')])
-clean.report[clean.report$Sample.Name == 'Ara.Mix', 'Sample.Type'] <- 'QC.Standard'
-collect.reports[[report.name]] <- clean.report
-#
-# ################################################################################################################
-# ### Plot the response of all samples against the response in blank
-# ################################################################################################################
-#
-# pdf(paste(nice.date, "QC_ComparisonBlankIndividual.pdf", sep = '_'), width = 9, height = 6)
-#
-# for(i in sort(unique(clean.report$Compound)))
-# {
-#
-# compound.sub <- subset(clean.report, Sample.Type != 'Standard' & Compound == i)
-# t.tests <- c()
-# for(m in unique(compound.sub$Acq.Method.Condensed))
-# {
-#
-# x <- subset(compound.sub, Acq.Method.Condensed == m)
-#
-# blank <- subset(x, Sample.Type == 'Blank', Resp, drop = T)
-# samples <- subset(x, Sample.Type == 'Sample', Resp, drop = T)
-#
-# FC <- round(mean(samples) / mean(blank), 1)
-#
-# if(length(blank) > 2 & length(samples) > 2){p <- signif(t.test(blank, samples)$p.value, 3)}else{p <- ''}
-#
-#
-# t.tests <- rbind(t.tests, data.frame(FC, p, Acq.Method.Condensed = m, Resp = (max(samples))))
-# }
-#
-#
-# print(
-# ggplot(compound.sub, aes(x = Sample.Type, y = Resp)) +
-# geom_boxplot() +
-# geom_text(data = t.tests, x = 1 , vjust = 1, aes(label = paste(FC, 'x \np: ', p, sep = ''))) +
-# theme_dominik +
-# facet_wrap(~Acq.Method.Condensed, scales = "free", labeller = label_parsed) +
-# labs(y = 'non-normalized response', caption = wd) +
-# # scale_color_brewer(palette = "Dark2") +
-# ggtitle(parse(text = i))
-# )
-#
-# }
-#
-# dev.off()
-#
-#
-scaled.within.compound <- c()
-for(i in unique(clean.report$Compound))
-{
-sub <- subset(clean.report, Compound == i)
-sub$sResp <- sub$Resp / max(sub$Resp)
-scaled.within.compound <- rbind(scaled.within.compound, sub)
-}
-scaled.within.compound$Compound <- factor(scaled.within.compound$Compound, levels = sort(unique(scaled.within.compound$Compound)))
-print(ggplot(subset(scaled.within.compound, Sample.Type != 'Standard'), aes(x = Compound, y = Resp)) +
-geom_boxplot(aes(fill = Sample.Type)) +
-theme_dominik +
-facet_wrap(~Acq.Method.Condensed, scales = "free_y", ncol = 1) +
-labs(y = 'non-normalized response\nscaled by compound', caption = wd) +
-theme(aspect.ratio = 0.5, axis.text.x = element_text(angle = 45, hjust = 1)) +
-scale_x_discrete(labels = parse(text = as.character(levels(scaled.within.compound$Compound)))) +
-scale_fill_brewer(palette = "Dark2"))
-a <- dcast(subset(clean.report, Sample.Type == 'Sample'), Sample.Name~Compound, value.var = 'Resp')
-clean.report$Compound <- factor(clean.report$Compound, levels = names(sort(apply(a[, 2 : ncol(a)], 2, max))))
-print(
-ggplot(subset(clean.report, Sample.Type == 'Sample'), aes(x = Compound, y = Resp, label = Sample.Name)) +
-geom_text(size = 4) +
-theme_dominik +
-facet_wrap(~Acq.Method.Condensed, scales = "free_y", ncol = 1) +
-labs(y = 'non-normalized response', caption = wd) +
-theme(aspect.ratio = 1, axis.text.x = element_text(angle = 45, hjust = 1)) +
-scale_x_discrete(labels = parse(text = as.character(levels(clean.report$Compound)))) +
-scale_fill_brewer(palette = "Dark2")
-)
-clean.report$Compound <- gsub("'", "", clean.report$Compound, fixed = T)
-collect.reports[[report.name]] <- clean.report
-}
-dev.off()
-names(collect.reports) <- paste0('Report', 1:length(collect.reports))
-write.xlsx(collect.reports, asTable = T, file = paste(nice.date, "CleanReports.xlsx", sep = '_'))
diff --git a/cmml/18-0008_Eva_Maleckova/GC-MS/181204_DoubleChecked/181204_CleanReport.xlsx b/cmml/18-0008_Eva_Maleckova/GC-MS/181204_DoubleChecked/181204_CleanReport.xlsx
deleted file mode 100755
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diff --git a/cmml/18-0008_Eva_Maleckova/GC-MS/181204_DoubleChecked/181204_QC_QuantReport.R b/cmml/18-0008_Eva_Maleckova/GC-MS/181204_DoubleChecked/181204_QC_QuantReport.R
deleted file mode 100755
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--- a/cmml/18-0008_Eva_Maleckova/GC-MS/181204_DoubleChecked/181204_QC_QuantReport.R
+++ /dev/null
@@ -1,201 +0,0 @@
-
-rm(list = ls())
-
-### Mac dir tree or ### PC dir tree
-if(dir.exists('/Volumes/data/')){setwd('/Volumes/data/')}; if(dir.exists('M:/MSlab/')){setwd('M:/')}
-
-source('MSlab/19_MS-Team/05_Dominik_Brilhaus/00_CustomR_Functions/01_MSLab.R')
-
-wd <- 'MSlab/21_projects/18-0008_Eva_Maleckova/GC-MS/181204_DoubleChecked/'
-setwd(wd)
-
-#################################################
-
-required.packages <- c("Rmisc", "plyr", "ggplot2", "reshape2", "gridExtra", 'openxlsx')
-
-for(package in required.packages)
-{
- print(package)
- ## Check if package is installed. If not, install
- if(!package %in% row.names(installed.packages())){install.packages(package, repos ="https://cran.uni-muenster.de/")}
- # ## Check if package is up to date. If not, update
- # update.packages(package, repos = "https://cran.uni-muenster.de/")
- ## Load package
- library(package, character.only = T)
-}
-
-
-theme_dominik <-
- theme(panel.grid = element_blank(), panel.background = element_blank(), panel.border = element_rect(fill = NA)) +
- theme(axis.text = element_text(color = "black"), axis.ticks = element_line(color = "black"), axis.title = element_text(color = "black")) +
- theme(plot.title = element_text(face= "bold")) +
- theme(aspect.ratio = 1) +
- theme(strip.background = element_blank(), strip.text = element_text(size = 10, face = "bold")) +
- theme(legend.position = "right", legend.title = element_blank()) #legend.direction = "vertical",
-
-nice.date <- format(Sys.time(), "%y%m%d")
-
-
-#################################################
-### Identify quant report
-
-report.xlsx <- dir(pattern = 'QuantReport')
-report.xlsx <- grep('xlsx', value = T, report.xlsx)
-
-collect.reports <- list()
-
-pdf(paste(nice.date, "QC_QuantReport.pdf", sep = '_'), width = 15, height = 15)
-for(report.name in report.xlsx)
-{
-
- ## Load QuantReport book
-
-
- GC.report <- read.xlsx(report.name, "Summary")
- clean.report <- report.extract(GC.report)
- clean.report$data.source <- report.name
-
- colnames(clean.report) <- gsub(' ', '.', colnames(clean.report))
-
-
- ### Rename compounds
- clean.report$Compound <- gsub("Gaba", "GABA", clean.report$Compound)
- clean.report$Compound <- gsub("a ", "alpha-", clean.report$Compound)
- clean.report$Compound <- gsub("b ", "beta-", clean.report$Compound)
- clean.report$Compound <- gsub("ic Acid", "ate", clean.report$Compound)
- clean.report$Compound <- gsub(" 2TMS", "", clean.report$Compound)
- # clean.report$Compound <- gsub(" 3TMS", "", clean.report$Compound)
-
- clean.report[!grepl("alpha-", clean.report$Compound) & !grepl("beta-", clean.report$Compound), "Compound"] <- paste("'", clean.report[!grepl("alpha-", clean.report$Compound) & !grepl("beta-", clean.report$Compound), "Compound"], "'", sep = "")
-
- colnames(clean.report) <- gsub(" ", ".", colnames(clean.report))
-
-
- #### Distinguish between split and splitless
- #### and keep only those compounds that passed the manual qc
-
- split.df <- data.frame(Acq.Method.File = unique(clean.report$Acq.Method.File))
- split.df[grepl("split", unique(split.df$Acq.Method.File), ignore.case = T) & !grepl("splitles", unique(split.df$Acq.Method.File), ignore.case = T), "Acq.Method.Condensed"] <- "split"
- split.df[grepl("splitles", unique(split.df$Acq.Method.File), ignore.case = T), "Acq.Method.Condensed"] <- "splitless"
-
- ###
- warning("Double-check correct assignment of split / splitless")
- print(split.df)
-
- clean.report <- merge(clean.report, split.df, "Acq.Method.File")
-
-
- unique(clean.report[, c('Sample.Type','Sample.Name')])
-
- clean.report[clean.report$Sample.Name == 'Ara.Mix', 'Sample.Type'] <- 'QC.Standard'
-
-
-
- collect.reports[[report.name]] <- clean.report
-
-
-
-
- #
- # ################################################################################################################
- # ### Plot the response of all samples against the response in blank
- # ################################################################################################################
- #
- # pdf(paste(nice.date, "QC_ComparisonBlankIndividual.pdf", sep = '_'), width = 9, height = 6)
- #
- # for(i in sort(unique(clean.report$Compound)))
- # {
- #
- # compound.sub <- subset(clean.report, Sample.Type != 'Standard' & Compound == i)
- # t.tests <- c()
- # for(m in unique(compound.sub$Acq.Method.Condensed))
- # {
- #
- # x <- subset(compound.sub, Acq.Method.Condensed == m)
- #
- # blank <- subset(x, Sample.Type == 'Blank', Resp, drop = T)
- # samples <- subset(x, Sample.Type == 'Sample', Resp, drop = T)
- #
- # FC <- round(mean(samples) / mean(blank), 1)
- #
- # if(length(blank) > 2 & length(samples) > 2){p <- signif(t.test(blank, samples)$p.value, 3)}else{p <- ''}
- #
- #
- # t.tests <- rbind(t.tests, data.frame(FC, p, Acq.Method.Condensed = m, Resp = (max(samples))))
- # }
- #
- #
- # print(
- # ggplot(compound.sub, aes(x = Sample.Type, y = Resp)) +
- # geom_boxplot() +
- # geom_text(data = t.tests, x = 1 , vjust = 1, aes(label = paste(FC, 'x \np: ', p, sep = ''))) +
- # theme_dominik +
- # facet_wrap(~Acq.Method.Condensed, scales = "free", labeller = label_parsed) +
- # labs(y = 'non-normalized response', caption = wd) +
- # # scale_color_brewer(palette = "Dark2") +
- # ggtitle(parse(text = i))
- # )
- #
- # }
- #
- # dev.off()
- #
- #
-
-
- scaled.within.compound <- c()
- for(i in unique(clean.report$Compound))
- {
- sub <- subset(clean.report, Compound == i)
-
-
- sub$sResp <- sub$Resp / max(sub$Resp)
-
- scaled.within.compound <- rbind(scaled.within.compound, sub)
-
- }
-
- scaled.within.compound$Compound <- factor(scaled.within.compound$Compound, levels = sort(unique(scaled.within.compound$Compound)))
-
-
- print(ggplot(subset(scaled.within.compound, Sample.Type != 'Standard'), aes(x = Compound, y = Resp)) +
- geom_boxplot(aes(fill = Sample.Type)) +
- theme_dominik +
- facet_wrap(~Acq.Method.Condensed, scales = "free_y", ncol = 1) +
- labs(y = 'non-normalized response\nscaled by compound', caption = wd) +
- theme(aspect.ratio = 0.5, axis.text.x = element_text(angle = 45, hjust = 1)) +
- scale_x_discrete(labels = parse(text = as.character(levels(scaled.within.compound$Compound)))) +
- scale_fill_brewer(palette = "Dark2"))
-
-
- a <- dcast(subset(clean.report, Sample.Type == 'Sample'), Sample.Name~Compound, value.var = 'Resp')
- clean.report$Compound <- factor(clean.report$Compound, levels = names(sort(apply(a[, 2 : ncol(a)], 2, max))))
-
-
-
- print(
- ggplot(subset(clean.report, Sample.Type == 'Sample'), aes(x = Compound, y = Resp, label = Sample.Name)) +
- geom_text(size = 4) +
- theme_dominik +
- facet_wrap(~Acq.Method.Condensed, scales = "free_y", ncol = 1) +
- labs(y = 'non-normalized response', caption = wd) +
- theme(aspect.ratio = 1, axis.text.x = element_text(angle = 45, hjust = 1)) +
- scale_x_discrete(labels = parse(text = as.character(levels(clean.report$Compound)))) +
- scale_fill_brewer(palette = "Dark2")
- )
-
- clean.report$Compound <- gsub("'", "", clean.report$Compound, fixed = T)
- collect.reports[[report.name]] <- clean.report
-
-
-}
-dev.off()
-
-
-names(collect.reports) <- paste0('Report', 1:length(collect.reports))
-
-write.xlsx(collect.reports, asTable = T, file = paste(nice.date, "CleanReports.xlsx", sep = '_'))
-
-
-
-
diff --git a/cmml/18-0008_Eva_Maleckova/GC-MS/181204_DoubleChecked/181204_QC_QuantReport.pdf b/cmml/18-0008_Eva_Maleckova/GC-MS/181204_DoubleChecked/181204_QC_QuantReport.pdf
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diff --git a/cmml/18-0008_Eva_Maleckova/GC-MS/2018-03-07_MetabolitesQuickView.pdf b/cmml/18-0008_Eva_Maleckova/GC-MS/2018-03-07_MetabolitesQuickView.pdf
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diff --git a/cmml/18-0008_Eva_Maleckova/GC-MS/EM-GC-MS_project_info_180008.xlsx b/cmml/18-0008_Eva_Maleckova/GC-MS/EM-GC-MS_project_info_180008.xlsx
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diff --git a/cmml/18-0008_Eva_Maleckova/GC-MS/Thumbs.db b/cmml/18-0008_Eva_Maleckova/GC-MS/Thumbs.db
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diff --git a/cmml/18-0008_Eva_Maleckova/LC-QTof/180620_Eva_01.xls b/cmml/18-0008_Eva_Maleckova/LC-QTof/180620_Eva_01.xls
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diff --git a/cmml/18-0008_Eva_Maleckova/LC-QTof/180621_Eva_02.xls b/cmml/18-0008_Eva_Maleckova/LC-QTof/180621_Eva_02.xls
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD/.Rhistory b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD/.Rhistory
deleted file mode 100755
index 870d1c284a05fbad44fca0f4417f486f3eee4b3a..0000000000000000000000000000000000000000
--- a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD/.Rhistory
+++ /dev/null
@@ -1,151 +0,0 @@
-setwd("/Volumes/data/MSlab/05_projects/18-0008_Eva_Maleckova/UHPLC-DAD/")
-rm(list = ls())
-library(readxl)
-lc.report <- "180612-EvaReport.xlsx"
-report.summmary <- list()
-for(i in excel_sheets(lc.report))
-{
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-if(!current.sheet[1, 2] %in% c("Blank", "blank"))
-{
-info.table <- c()
-for(row in 1:(which(current.sheet[, 1] == 'Name')-1) )
-{
-x <- current.sheet[row, 1:5]
-y <- x[!is.na(x)]
-if(length(y) == 2){info.table <- c(info.table, y)}
-if(length(y) == 1){info.table <- c(info.table, c(y, 'NA'))}
-x <- current.sheet[row, 6:ncol(current.sheet)]
-y <- x[!is.na(x)]
-if(length(y) == 2){info.table <- c(info.table, y)}
-if(length(y) == 1){info.table <- c(info.table, c(y, 'NA'))}
-}
-info <- t(data.frame('a' = info.table[seq(1, length(info.table), 2)], 'b' = info.table[seq(2, length(info.table), 2)]))
-type <- info['b', 8]
-sample.data <- current.sheet[which(current.sheet[, 1] == 'Name'):(nrow(current.sheet)-1), ]
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1, !is.na(colnames(sample.data))]
-sample.data <- sample.data[, apply(sample.data, 2, function(x){sum(is.na(x)) != nrow(sample.data)})]
-colnames(sample.data)[c(1, 5, 6)] <- c("Compound", "Amount_pmol", "Concentration_pmol.µl")
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-}
-}
-excel_sheets(lc.report)
-View(all.data)
-report.summmary <- list()
-for(i in excel_sheets(lc.report))
-{
-print(i)
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-if(!current.sheet[1, 2] %in% c("Blank", "blank"))
-{
-info.table <- c()
-for(row in 1:(which(current.sheet[, 1] == 'Name')-1) )
-{
-x <- current.sheet[row, 1:5]
-y <- x[!is.na(x)]
-if(length(y) == 2){info.table <- c(info.table, y)}
-if(length(y) == 1){info.table <- c(info.table, c(y, 'NA'))}
-x <- current.sheet[row, 6:ncol(current.sheet)]
-y <- x[!is.na(x)]
-if(length(y) == 2){info.table <- c(info.table, y)}
-if(length(y) == 1){info.table <- c(info.table, c(y, 'NA'))}
-}
-info <- t(data.frame('a' = info.table[seq(1, length(info.table), 2)], 'b' = info.table[seq(2, length(info.table), 2)]))
-type <- info['b', 8]
-sample.data <- current.sheet[which(current.sheet[, 1] == 'Name'):(nrow(current.sheet)-1), ]
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1, !is.na(colnames(sample.data))]
-sample.data <- sample.data[, apply(sample.data, 2, function(x){sum(is.na(x)) != nrow(sample.data)})]
-colnames(sample.data)[c(1, 5, 6)] <- c("Compound", "Amount_pmol", "Concentration_pmol.µl")
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-}
-}
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-View(current.sheet)
-!current.sheet[1, 2] %in% c("Blank", "blank")
-current.sheet[1, 2]
-which(current.sheet[, 1] == 'Name')
-current.sheet[, 1] == 'Name'
-length(which(current.sheet[, 1] == 'Name'))
-length(which(current.sheet[, 1] == 'Name')) != 0
-report.summmary <- list()
-for(i in excel_sheets(lc.report))
-{
-print(i)
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-if(!current.sheet[1, 2] %in% c("Blank", "blank") & length(which(current.sheet[, 1] == 'Name')) != 0 )
-{
-info.table <- c()
-for(row in 1:(which(current.sheet[, 1] == 'Name')-1) )
-{
-x <- current.sheet[row, 1:5]
-y <- x[!is.na(x)]
-if(length(y) == 2){info.table <- c(info.table, y)}
-if(length(y) == 1){info.table <- c(info.table, c(y, 'NA'))}
-x <- current.sheet[row, 6:ncol(current.sheet)]
-y <- x[!is.na(x)]
-if(length(y) == 2){info.table <- c(info.table, y)}
-if(length(y) == 1){info.table <- c(info.table, c(y, 'NA'))}
-}
-info <- t(data.frame('a' = info.table[seq(1, length(info.table), 2)], 'b' = info.table[seq(2, length(info.table), 2)]))
-type <- info['b', 8]
-sample.data <- current.sheet[which(current.sheet[, 1] == 'Name'):(nrow(current.sheet)-1), ]
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1, !is.na(colnames(sample.data))]
-sample.data <- sample.data[, apply(sample.data, 2, function(x){sum(is.na(x)) != nrow(sample.data)})]
-colnames(sample.data)[c(1, 5, 6)] <- c("Compound", "Amount_pmol", "Concentration_pmol.µl")
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-}
-}
-final.summary <- list()
-for(type in names(report.summmary))
-{
-final.summary[[type]] <- do.call(rbind, report.summmary[[type]])
-}
-View(final.summary)
-View(final.summary$Sample)
-View(final.summary$Calibration)
-current.sheet <- as.data.frame(read.xlsx(lc.report, sheet = i, colNames = F))
-library(openxlsx)
-current.sheet <- as.data.frame(read.xlsx(lc.report, sheet = i, colNames = F))
-print(i)
-i
-lc.report
-i <- 'Page 3'
-read.xlsx(lc.report, sheet = i, colNames = F)
-library(readxl)
-library(openxlsx)
-nice.date <- format(Sys.time(), "%y%m%d")
-nice.date
-write.xlsx(final.summary, file = paste(nice.date,'HPLC_DAD_AA_Data.xlsx', sep = '_'), asTable = F, colNames = T, creator = 'dominik.brilhaus@hhu.de')
diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD/01UHPLC-DAD_Scram.R b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD/01UHPLC-DAD_Scram.R
deleted file mode 100755
index 81fbfd7451f4d231a3458a06e05185bc8e9e887b..0000000000000000000000000000000000000000
--- a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD/01UHPLC-DAD_Scram.R
+++ /dev/null
@@ -1,89 +0,0 @@
-
-
-
-setwd("/Volumes/data/MSlab/21_projects/18-0008_Eva_Maleckova/UHPLC-DAD/")
-rm(list = ls())
-
-library(readxl)
-library(openxlsx)
-
-nice.date <- format(Sys.time(), "%y%m%d")
-
-lc.report <- "180612-EvaReport.xlsx"
-
-
-report.summmary <- list()
-for(i in excel_sheets(lc.report))
-{
- print(i)
-
- current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-
- if(!current.sheet[1, 2] %in% c("Blank", "blank") & length(which(current.sheet[, 1] == 'Name')) != 0 )
- {
-
- info.table <- c()
- for(row in 1:(which(current.sheet[, 1] == 'Name')-1) )
- {
-
- x <- current.sheet[row, 1:5]
- y <- x[!is.na(x)]
- if(length(y) == 2){info.table <- c(info.table, y)}
- if(length(y) == 1){info.table <- c(info.table, c(y, 'NA'))}
-
- x <- current.sheet[row, 6:ncol(current.sheet)]
- y <- x[!is.na(x)]
- if(length(y) == 2){info.table <- c(info.table, y)}
- if(length(y) == 1){info.table <- c(info.table, c(y, 'NA'))}
-
- }
-
- info <- t(data.frame('a' = info.table[seq(1, length(info.table), 2)], 'b' = info.table[seq(2, length(info.table), 2)]))
-
- type <- info['b', 8]
-
- sample.data <- current.sheet[which(current.sheet[, 1] == 'Name'):(nrow(current.sheet)-1), ]
- colnames(sample.data) <- sample.data[1,]
- sample.data <- sample.data[-1, !is.na(colnames(sample.data))]
-
- sample.data <- sample.data[, apply(sample.data, 2, function(x){sum(is.na(x)) != nrow(sample.data)})]
-
- colnames(sample.data)[c(1, 5, 6)] <- c("Compound", "Amount_pmol", "Concentration_pmol.µl")
-
- sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-
- duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
- colnames(duplicated.info) <- gsub(":", "", info[1,])
- for(j in 1:nrow(sample.data))
- {
- duplicated.info <- rbind(duplicated.info, info[2,])
- }
- duplicated.info <- duplicated.info[-1,]
-
- all.data <- cbind.data.frame(duplicated.info, sample.data)
- colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-
- report.summmary[[type]][[i]] <- all.data
-
- }
-
-}
-
-
-final.summary <- list()
-for(type in names(report.summmary))
-{
- final.summary[[type]] <- do.call(rbind, report.summmary[[type]])
-
-
-}
-
-
-save(final.summary, file = "01.UHPLC.RData")
-
-
-
-write.xlsx(final.summary, file = paste(nice.date,'HPLC_DAD_AA_Data.xlsx', sep = '_'), asTable = F, colNames = T, creator = 'dominik.brilhaus@hhu.de')
-
-
-
diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD/180612-EvaReport.pdf b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD/180612-EvaReport.pdf
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD/180612-EvaReport.xlsx b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD/180612-EvaReport.xlsx
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD/180612_HPLC_DAD_AA_Data.xlsx b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD/180612_HPLC_DAD_AA_Data.xlsx
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD/Maleckova-AminoAcidsProjectSheet-2018_05_11-complete.xlsx b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD/Maleckova-AminoAcidsProjectSheet-2018_05_11-complete.xlsx
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/.DS_Store b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/.DS_Store
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/.Rhistory b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/.Rhistory
deleted file mode 100755
index 59a2aba1c0d772311563dffc08a88d2172eed0c3..0000000000000000000000000000000000000000
--- a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/.Rhistory
+++ /dev/null
@@ -1,512 +0,0 @@
-calib$Amount <- as.numeric(calib$Amount)
-p1 <- ggplot(calib, aes(x = std.amount, y = Amount)) +
-geom_point() +
-facet_wrap(~Compound) +
-theme_classic()
-sample.data <- merge(final.summary$Sample, sample.list, by.x = "Sample.name", by.y = "Sample.label.on.tube")
-condi.colnames <- c("Condition.1", "Condition.2")
-### Create a group variable based on sample list (e.g. different species, conditions, treatments, etc.)
-if(length(condi.colnames) > 1)
-{sample.data$GroupVar <- apply(sample.data[,condi.colnames], 1, function(x){paste(x, collapse = "\n")})
-}else{
-sample.data$GroupVar <- sample.data[,condi.colnames]
-}
-sample.data$GroupVar <- factor(sample.data$GroupVar, levels = unique(sample.data[order(sample.data[,condi.colnames[1]]), "GroupVar"]))
-p2 <- ggplot(sample.data, aes(x = GroupVar, y = Amount)) +
-geom_point() +
-facet_wrap(~Compound) +
-theme_classic()
-pdf("Test.pdf",width = 12, height = 12)
-p2
-dev.off()
-sample.data$Amount <- as.numeric(sample.data$Amount)
-p2 <- ggplot(sample.data, aes(x = GroupVar, y = Amount)) +
-geom_point() +
-facet_wrap(~Compound) +
-theme_classic()
-pdf("Test.pdf",width = 12, height = 12)
-p2
-dev.off()
-p2 <- ggplot(sample.data, aes(x = GroupVar, y = Amount)) +
-geom_point() +
-facet_wrap(~Compound, scales = "free") +
-theme_classic()
-pdf("Test.pdf",width = 12, height = 12)
-p2
-dev.off()
-p2 <- ggplot(sample.data, aes(x = GroupVar, y = Amount)) +
-geom_point() +
-facet_wrap(~Compound, scales = "free") +
-theme_dominik
-pdf("Test.pdf",width = 12, height = 12)
-p2
-dev.off()
-sample.data$pmol.mg.FW <- sample.data$Amount / sample.data$Sample.weight..mg.
-sample.data$pmol.mg.FW
-sample.data$pmol.g.FW <- sample.data$Amount / sample.data$Sample.weight..mg. * 1000
-sample.data$pmol.g.FW
-sample.data$pmol.mg.FW <- sample.data$Amount / sample.data$Sample.weight..mg.
-sample.data$µmol.g.FW <- sample.data$Amount / sample.data$Sample.weight..mg.
-sample.data$µmol.g.FW
-sample.data$µmol.mg.FW <- sample.data$Amount / sample.data$Sample.weight..mg. * 1000
-sample.data$µmol.mg.FW
-p2 <- ggplot(sample.data, aes(x = GroupVar, y = µmol.mg.FW)) +
-geom_point() +
-facet_wrap(~Compound, scales = "free") +
-theme_dominik
-pdf("Test.pdf",width = 12, height = 12)
-p2
-dev.off()
-pdf("EvaAA.pdf",width = 12, height = 12)
-p2
-dev.off()
-setwd("/Volumes/data/MSlab/05_projects/18-0008_Eva_Maleckova/UHPLC-DAD/")
-rm(list = ls())
-library(XLConnect)
-lc.report <- loadWorkbook("2018-03-14_EvaReport.xlsx")
-report.summmary <- list()
-for(i in getSheets(lc.report))
-{
-current.sheet <- readWorksheet(lc.report, i, header = F)
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-type <- info2$b[3]
-sample.data <- current.sheet[14:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]
-if(type == "Calibration"){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1,]
-colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-}
-sample.data
-type
-i
-i <- "Page 2"
-getSheets(lc.report)
-current.sheet <- readWorksheet(lc.report, i, header = F)
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-type <- info2$b[3]
-type
-i <- "Page 14"
-current.sheet <- readWorksheet(lc.report, i, header = F)
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-type <- info2$b[3]
-sample.data <- current.sheet[14:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]
-if(type == "Calibration"){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1,]
-colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-sample.data
-sample.data[,2:6]
-as.matrix(sample.data[,2:6])
-as.numeric(sample.data[,2:6])
-apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-sample.data[,2:6]
-sample.data$Concentration
-lc.report <- loadWorkbook("2018-03-14_EvaReport.xlsx")
-report.summmary <- list()
-for(i in getSheets(lc.report))
-{
-current.sheet <- readWorksheet(lc.report, i, header = F)
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-type <- info2$b[3]
-sample.data <- current.sheet[14:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]
-if(type == "Calibration"){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1,]
-colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-}
-current.sheet <- readWorksheet(lc.report, i, header = F)
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-info2 <- current.sheet[3:5, c(9, 11)]
-current.sheet
-report.summmary <- list()
-for(i in getSheets(lc.report))
-{
-current.sheet <- readWorksheet(lc.report, i, header = F)
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-type <- info2$b[3]
-sample.data <- current.sheet[14:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]
-if(type == "Calibration"){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1,]
-colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-}
-final.summary <- list()
-for(type in names(report.summmary))
-{
-final.summary[[type]] <- do.call(rbind, report.summmary[[type]])
-}
-############################
-#### Export data
-xlcFreeMemory()
-Data.xlsx <- loadWorkbook(paste(Sys.Date(), "01.Data.xlsx", sep = "_"), create = TRUE)
-createSheet(Data.xlsx, "SampleData")
-writeWorksheet(Data.xlsx, final.summary$Sample, "SampleData")
-saveWorkbook(Data.xlsx)
-createSheet(Data.xlsx, "Calibration")
-writeWorksheet(Data.xlsx, final.summary$Calibration, "Calibration")
-saveWorkbook(Data.xlsx)
-createSheet(Data.xlsx, "Blank")
-writeWorksheet(Data.xlsx, final.summary$Blank, "Blank")
-saveWorkbook(Data.xlsx)
-save(final.summary, file = "01.UHPLC.RData")
-setwd("/Volumes/data/MSlab/05_projects/18-0008_Eva_Maleckova/UHPLC-DAD/")
-rm(list = ls())
-required.packages <- c("Rmisc", "plyr", "ggplot2", "XLConnect","reshape2", "gridExtra")
-for(package in required.packages)
-{
-print(package)
-## Check if package is installed. If not, install
-if(!package %in% row.names(installed.packages())){install.packages(package, repos ="https://cran.uni-muenster.de/")}
-# ## Check if package is up to date. If not, update
-# update.packages(package, repos = "https://cran.uni-muenster.de/")
-## Load package
-library(package, character.only = T)
-}
-theme_dominik <-
-theme(panel.grid = element_blank(), panel.background = element_blank(), panel.border = element_rect(fill = NA)) +
-theme(axis.text = element_text(color = "black"), axis.ticks = element_line(color = "black"), axis.title = element_text(color = "black")) +
-theme(plot.title = element_text(face= "bold")) +
-theme(aspect.ratio = 1) +
-theme(strip.background = element_blank(), strip.text = element_text(size = 10, face = "bold")) +
-theme(legend.position = "bottom", legend.direction = "horizontal", legend.title = element_blank())
-load("01.UHPLC.RData")
-calib <- final.summary$Calibration
-calib$std.amount <- as.numeric(do.call(rbind, strsplit(calib$Sample.name, split = " "))[,1])
-p1 <- ggplot(calib, aes(x = std.amount, y = Amount)) +
-geom_point() +
-facet_wrap(~Compound) +
-theme_classic()
-sample.list <- readWorksheetFromFile("AAs-HPLC-test-2018_02_21.xlsx", "Sample info")
-sample.data <- merge(final.summary$Sample, sample.list, by.x = "Sample.name", by.y = "Sample.label.on.tube")
-pdf("02.1CalibrationCurves.pdf",width = 12, height = 12)
-p2
-dev.off()
-p1 <- ggplot(calib, aes(x = std.amount, y = Amount)) +
-geom_point() +
-facet_wrap(~Compound) +
-theme_classic()
-pdf("02.1CalibrationCurves.pdf",width = 12, height = 12)
-p1
-dev.off()
-p1 <- ggplot(calib, aes(x = std.amount, y = Amount)) +
-geom_point() +
-facet_wrap(~Compound) +
-theme_dominik
-pdf("02.1CalibrationCurves.pdf",width = 12, height = 12)
-p1
-dev.off()
-theme_dominik <-
-theme(panel.background = element_blank(), panel.border = element_rect(fill = NA)) +
-theme(axis.text = element_text(color = "black"), axis.ticks = element_line(color = "black"), axis.title = element_text(color = "black")) +
-theme(plot.title = element_text(face= "bold")) +
-theme(aspect.ratio = 1) +
-theme(strip.background = element_blank(), strip.text = element_text(size = 10, face = "bold")) +
-theme(legend.position = "bottom", legend.direction = "horizontal", legend.title = element_blank())
-p1 <- ggplot(calib, aes(x = std.amount, y = Amount)) +
-geom_point() +
-facet_wrap(~Compound) +
-theme_dominik
-pdf("02.1CalibrationCurves.pdf",width = 12, height = 12)
-p1
-dev.off()
-theme_dominik <-
-theme(panel.background = element_blank(), panel.border = element_rect(fill = NA)) +
-theme(axis.text = element_text(color = "black"), axis.ticks = element_line(color = "black"), axis.title = element_text(color = "black")) +
-theme(plot.title = element_text(face= "bold")) +
-theme(aspect.ratio = 1) +
-theme(strip.background = element_blank(), strip.text = element_text(size = 10, face = "bold")) +
-theme(legend.position = "bottom", legend.direction = "horizontal", legend.title = element_blank())
-p1 <- ggplot(calib, aes(x = std.amount, y = Amount)) +
-geom_point() +
-facet_wrap(~Compound) +
-theme_dominik
-pdf("02.1CalibrationCurves.pdf",width = 12, height = 12)
-p1
-dev.off()
-p1 <- ggplot(calib, aes(x = std.amount, y = Amount)) +
-geom_point() +
-facet_wrap(~Compound) +
-theme_dominik + theme(panel.grid.major = element_line(colour = "grey"))
-pdf("02.1CalibrationCurves.pdf",width = 12, height = 12)
-p1
-dev.off()
-ggplotRegression <- function (fit) {
-ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
-stat_smooth(method = "lm", col = "firebrick") +
-geom_point() +
-annotate("text", x= 0, y = 0.5, hjust = 0, vjust = 1, label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 2),
-"\nIntercept =",signif(fit$coef[[1]],2 ),
-"\nSlope =",signif(fit$coef[[2]], 2),
-"\nP =",signif(summary(fit)$coef[2,4], 2)), size = 2) +
-theme_dominik
-}
-calib
-ggplotRegression(subset(calib, Compound == "Serine"))
-subset(calib, Compound == "Serine")
-lm(std.amount ~ Amount, data = subset(calib, Compound == "Serine"))
-ggplotRegression(lm(std.amount ~ Amount, data = subset(calib, Compound == "Serine")))
-ggplotRegression <- function (fit) {
-ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
-stat_smooth(method = "lm", col = "firebrick") +
-geom_point() +
-ggtitle(label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
-"Intercept =",signif(fit$coef[[1]],2 ),
-"Slope =",signif(fit$coef[[2]], 2),
-"P =",signif(summary(fit)$coef[2,4], 2), sep = "\n")) +
-theme_dominik
-}
-ggplotRegression(lm(std.amount ~ Amount, data = subset(calib, Compound == "Serine")))
-ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
-stat_smooth(method = "lm", col = "firebrick") +
-geom_point() +
-ggtitle(label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
-"\nIntercept =",signif(fit$coef[[1]],2 ),
-"\nSlope =",signif(fit$coef[[2]], 2),
-"\nP =",signif(summary(fit)$coef[2,4], 2))) +
-theme_dominik
-ggplotRegression <- function (fit) {
-ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
-stat_smooth(method = "lm", col = "firebrick") +
-geom_point() +
-ggtitle(label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
-"\nIntercept =",signif(fit$coef[[1]],2 ),
-"\nSlope =",signif(fit$coef[[2]], 2),
-"\nP =",signif(summary(fit)$coef[2,4], 2))) +
-theme_dominik
-}
-ggplotRegression(lm(std.amount ~ Amount, data = subset(calib, Compound == "Serine")))
-}
-}
-ggplotRegression <- function (fit) {
-ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
-stat_smooth(method = "lm", col = "firebrick") +
-geom_point() +
-ggtitle(label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
-# "\nIntercept =",signif(fit$coef[[1]],2 ),
-"\nSlope =",signif(fit$coef[[2]], 2))
-# "\nP =",signif(summary(fit)$coef[2,4], 2))
-) +
-theme_dominik
-}
-ggplotRegression(lm(std.amount ~ Amount, data = subset(calib, Compound == "Serine")))
-ggplotRegression <- function (fit) {
-ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
-stat_smooth(method = "lm", col = "firebrick") +
-geom_point(size = 2) +
-ggtitle(label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
-# "\nIntercept =",signif(fit$coef[[1]],2 ),
-"\nSlope =",signif(fit$coef[[2]], 2))
-# "\nP =",signif(summary(fit)$coef[2,4], 2))
-) +
-theme_dominik
-}
-ggplotRegression(lm(std.amount ~ Amount, data = subset(calib, Compound == "Serine")))
-lm(std.amount ~ Amount, data = subset(calib, Compound == "Serine"))
-fit <- lm(std.amount ~ Amount, data = subset(calib, Compound == "Serine"))
-fit
-fit$model
-max(fit$model[,1])
-ggplotRegression <- function (fit) {
-ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
-stat_smooth(method = "lm", col = "firebrick") +
-geom_point(size = 2) +
-annotate("text", x = min(fit$model[,2]), y = max(fit$model[,1]), label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
-# "\nIntercept =",signif(fit$coef[[1]],2 ),
-"\nSlope =",signif(fit$coef[[2]], 2))
-# "\nP =",signif(summary(fit)$coef[2,4], 2))
-) +
-theme_dominik
-}
-ggplotRegression(lm(std.amount ~ Amount, data = subset(calib, Compound == "Serine")))
-ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
-stat_smooth(method = "lm", col = "firebrick") +
-geom_point(size = 2) +
-annotate("text", x = min(fit$model[,2]), y = max(fit$model[,1]), hjust = 0, label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
-# "\nIntercept =",signif(fit$coef[[1]],2 ),
-"\nSlope =",signif(fit$coef[[2]], 2))
-# "\nP =",signif(summary(fit)$coef[2,4], 2))
-) +
-theme_dominik
-ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
-stat_smooth(method = "lm", col = "firebrick") +
-geom_point(size = 2) +
-annotate("text", x = min(fit$model[,2]), y = max(fit$model[,1]), hjust = 0, label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
-"\nIntercept =",signif(fit$coef[[1]],2 ),
-"\nSlope =",signif(fit$coef[[2]], 2))
-"\nP =",signif(summary(fit)$coef[2,4], 2))
-ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
-stat_smooth(method = "lm", col = "firebrick") +
-geom_point(size = 2) +
-annotate("text", x = min(fit$model[,2]), y = max(fit$model[,1]), hjust = 0, label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
-"\nIntercept =",signif(fit$coef[[1]],2 ),
-"\nSlope =",signif(fit$coef[[2]], 2),
-"\nP =",signif(summary(fit)$coef[2,4], 2))
-) +
-theme_dominik
-ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
-stat_smooth(method = "lm", col = "firebrick") +
-geom_point(size = 2) +
-annotate("text", x = min(fit$model[,2]), y = max(fit$model[,1]), hjust = 0, vjust = 0, label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
-"\nIntercept =",signif(fit$coef[[1]],2 ),
-"\nSlope =",signif(fit$coef[[2]], 2),
-"\nP =",signif(summary(fit)$coef[2,4], 2))
-) +
-theme_dominik
-ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
-stat_smooth(method = "lm", col = "firebrick") +
-geom_point(size = 2) +
-annotate("text", x = min(fit$model[,2]), y = max(fit$model[,1]), hjust = 0, vjust = 1, label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
-"\nIntercept =",signif(fit$coef[[1]],2 ),
-"\nSlope =",signif(fit$coef[[2]], 2),
-"\nP =",signif(summary(fit)$coef[2,4], 2))
-) +
-theme_dominik
-ggplotRegression <- function (fit) {
-ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
-stat_smooth(method = "lm", col = "firebrick") +
-geom_point(size = 2) +
-annotate("text", x = min(fit$model[,2]), y = max(fit$model[,1]), hjust = 0, vjust = 1, label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
-"\nIntercept =",signif(fit$coef[[1]],2 ),
-"\nSlope =",signif(fit$coef[[2]], 2),
-"\nP =",signif(summary(fit)$coef[2,4], 2))
-) +
-theme_dominik
-}
-calib.list <- list()
-calib.list <- list()
-for(cc in unique(calib$Compound))
-{
-calib.list[[cc]] <- ggplotRegression(lm(std.amount ~ Amount, data = subset(calib, Compound == cc)))
-}
-cc
-calib.list
-calib$Amount
-count(calib$Compound)
-View(calib)
-calib <- subset(calib, !is.na(Amount))
-count(calib$Compound)
-calib.list <- list()
-for(cc in unique(calib$Compound))
-{
-calib.list[[cc]] <- ggplotRegression(lm(std.amount ~ Amount, data = subset(calib, Compound == cc)))
-}
-cc
-View(calib)
-calib <- subset(calib, Sample.name == "200 pmol Mix")
-count(calib$Compound)
-calib <- final.summary$Calibration
-calib$std.amount <- as.numeric(do.call(rbind, strsplit(calib$Sample.name, split = " "))[,1])
-calib <- subset(calib, !is.na(Amount))
-calib <- subset(calib, Sample.name != "200 pmol Mix")
-count(calib$Compound)
-View(calib)
-calib.list <- list()
-for(cc in unique(calib$Compound))
-{
-calib.list[[cc]] <- ggplotRegression(lm(std.amount ~ Amount, data = subset(calib, Compound == cc)))
-}
-calib <- subset(calib, Compound == "Histidine")
-count(calib$Compound)
-calib <- final.summary$Calibration
-calib$std.amount <- as.numeric(do.call(rbind, strsplit(calib$Sample.name, split = " "))[,1])
-calib <- subset(calib, !is.na(Amount))
-calib <- subset(calib, Sample.name != "200 pmol Mix")
-calib <- subset(calib, Compound != "Histidine")
-count(calib$Compound)
-calib.list <- list()
-for(cc in unique(calib$Compound))
-{
-calib.list[[cc]] <- ggplotRegression(lm(std.amount ~ Amount, data = subset(calib, Compound == cc)))
-}
-p1 <- ggplot(calib, aes(x = std.amount, y = Amount)) +
-geom_point() +
-facet_wrap(~Compound) +
-theme_dominik + theme(panel.grid.major = element_line(colour = "grey"))
-pdf("02.1CalibrationCurves.pdf",width = 12, height = 12)
-do.call(grid.arrange, calib.list)
-dev.off()
-pdf("02.1CalibrationCurves.pdf",width = 20, height = 20)
-do.call(grid.arrange, calib.list)
-dev.off()
-calib.list <- list()
-for(cc in unique(calib$Compound))
-{
-calib.list[[cc]] <- ggplotRegression(lm(std.amount ~ Amount, data = subset(calib, Compound == cc))) + ggtitle(cc)
-}
-pdf("02.1CalibrationCurves.pdf",width = 20, height = 20)
-do.call(grid.arrange, calib.list)
-dev.off()
-sample.list <- readWorksheetFromFile("AAs-HPLC-test-2018_02_21.xlsx", "Sample info")
-sample.data <- merge(final.summary$Sample, sample.list, by.x = "Sample.name", by.y = "Sample.label.on.tube")
-condi.colnames <- c("Condition.1", "Condition.2")
-### Create a group variable based on sample list (e.g. different species, conditions, treatments, etc.)
-if(length(condi.colnames) > 1)
-{sample.data$GroupVar <- apply(sample.data[,condi.colnames], 1, function(x){paste(x, collapse = "\n")})
-}else{
-sample.data$GroupVar <- sample.data[,condi.colnames]
-}
-sample.data$GroupVar <- factor(sample.data$GroupVar, levels = unique(sample.data[order(sample.data[,condi.colnames[1]]), "GroupVar"]))
-sample.data$Amount <- as.numeric(sample.data$Amount)
-sample.data$µmol.mg.FW <- sample.data$Amount / sample.data$Sample.weight..mg. * 1000
-p2 <- ggplot(sample.data, aes(x = GroupVar, y = µmol.mg.FW)) +
-geom_point() +
-facet_wrap(~Compound, scales = "free") +
-theme_dominik
-pdf("02.2AminoAcids.pdf",width = 12, height = 12)
-p2
-dev.off()
diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/01.UHPLC.RData b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/01.UHPLC.RData
deleted file mode 100755
index dd134214b114a97246796efdb29236adac9309cc..0000000000000000000000000000000000000000
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/01UHPLC-DAD_Scram.R b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/01UHPLC-DAD_Scram.R
deleted file mode 100755
index 3cfbdfcae9677a2750ed44d946e97be2c880add7..0000000000000000000000000000000000000000
--- a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/01UHPLC-DAD_Scram.R
+++ /dev/null
@@ -1,89 +0,0 @@
-
-
-
-setwd("/Volumes/data/MSlab/21_projects/18-0008_Eva_Maleckova/UHPLC-DAD/")
-rm(list = ls())
-library(XLConnect)
-
-lc.report <- loadWorkbook("2018-03-14_EvaReport.xlsx")
-
-report.summmary <- list()
-for(i in getSheets(lc.report))
-{
-
- current.sheet <- readWorksheet(lc.report, i, header = F)
-
- info1 <- current.sheet[1:6, c(2, 5)]
- info2 <- current.sheet[3:5, c(9, 11)]
- info3 <- current.sheet[13, c(1, 3)]
-
- colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-
- info <- t(rbind(info1, info2, info3))
-
- type <- info2$b[3]
-
- sample.data <- current.sheet[14:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]
-
- if(type == "Calibration"){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-
- colnames(sample.data) <- sample.data[1,]
- sample.data <- sample.data[-1,]
-
- colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-
- sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-
- duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
- colnames(duplicated.info) <- gsub(":", "", info[1,])
- for(j in 1:nrow(sample.data))
- {
- duplicated.info <- rbind(duplicated.info, info[2,])
- }
- duplicated.info <- duplicated.info[-1,]
-
-
- all.data <- cbind.data.frame(duplicated.info, sample.data)
- colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-
- report.summmary[[type]][[i]] <- all.data
-
-}
-
-
-final.summary <- list()
-for(type in names(report.summmary))
-{
- final.summary[[type]] <- do.call(rbind, report.summmary[[type]])
-}
-
-
-
-############################
-#### Export data
-xlcFreeMemory()
-
-
-Data.xlsx <- loadWorkbook(paste(Sys.Date(), "01.Data.xlsx", sep = "_"), create = TRUE)
-
-createSheet(Data.xlsx, "SampleData")
-writeWorksheet(Data.xlsx, final.summary$Sample, "SampleData")
-saveWorkbook(Data.xlsx)
-
-createSheet(Data.xlsx, "Calibration")
-writeWorksheet(Data.xlsx, final.summary$Calibration, "Calibration")
-saveWorkbook(Data.xlsx)
-
-createSheet(Data.xlsx, "Blank")
-writeWorksheet(Data.xlsx, final.summary$Blank, "Blank")
-saveWorkbook(Data.xlsx)
-
-
-
-
-save(final.summary, file = "01.UHPLC.RData")
-
-
-
-
-
diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/02.1CalibrationCurves.pdf b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/02.1CalibrationCurves.pdf
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/02.2AminoAcids.pdf b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/02.2AminoAcids.pdf
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/02UHPLC.Analysis.R b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/02UHPLC.Analysis.R
deleted file mode 100755
index f2b3d0c120f9ad59af6dda543bdfba3bcf887782..0000000000000000000000000000000000000000
--- a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/02UHPLC.Analysis.R
+++ /dev/null
@@ -1,124 +0,0 @@
-
-
-setwd("/Volumes/data/MSlab/21_projects/18-0008_Eva_Maleckova/UHPLC-DAD/")
-rm(list = ls())
-
-
-#################################################
-
-required.packages <- c("Rmisc", "plyr", "ggplot2", "XLConnect","reshape2", "gridExtra")
-
-for(package in required.packages)
-{
- print(package)
- ## Check if package is installed. If not, install
- if(!package %in% row.names(installed.packages())){install.packages(package, repos ="https://cran.uni-muenster.de/")}
- # ## Check if package is up to date. If not, update
- # update.packages(package, repos = "https://cran.uni-muenster.de/")
- ## Load package
- library(package, character.only = T)
-}
-
-
-theme_dominik <-
- theme(panel.background = element_blank(), panel.border = element_rect(fill = NA)) +
- theme(axis.text = element_text(color = "black"), axis.ticks = element_line(color = "black"), axis.title = element_text(color = "black")) +
- theme(plot.title = element_text(face= "bold")) +
- theme(aspect.ratio = 1) +
- theme(strip.background = element_blank(), strip.text = element_text(size = 10, face = "bold")) +
- theme(legend.position = "bottom", legend.direction = "horizontal", legend.title = element_blank())
-
-ggplotRegression <- function (fit) {
-
- ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
- stat_smooth(method = "lm", col = "firebrick") +
- geom_point(size = 2) +
- annotate("text", x = min(fit$model[,2]), y = max(fit$model[,1]), hjust = 0, vjust = 1, label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
- "\nIntercept =",signif(fit$coef[[1]],2 ),
- "\nSlope =",signif(fit$coef[[2]], 2),
- "\nP =",signif(summary(fit)$coef[2,4], 2))
- ) +
- theme_dominik
-}
-
-
-
-
-load("01.UHPLC.RData")
-
-
-### Calibration curves
-
-
-calib <- final.summary$Calibration
-calib$std.amount <- as.numeric(do.call(rbind, strsplit(calib$Sample.name, split = " "))[,1])
-
-calib <- subset(calib, !is.na(Amount))
-calib <- subset(calib, Sample.name != "200 pmol Mix")
-
-calib <- subset(calib, Compound != "Histidine")
-
-count(calib$Compound)
-
-calib.list <- list()
-for(cc in unique(calib$Compound))
-{
- calib.list[[cc]] <- ggplotRegression(lm(std.amount ~ Amount, data = subset(calib, Compound == cc))) + ggtitle(cc)
-}
-
-
-
-# p1 <- ggplot(calib, aes(x = std.amount, y = Amount)) +
- # geom_point() +
- # facet_wrap(~Compound) +
- # theme_dominik + theme(panel.grid.major = element_line(colour = "grey"))
-
-
-pdf("02.1CalibrationCurves.pdf",width = 20, height = 20)
-do.call(grid.arrange, calib.list)
-dev.off()
-
-
-
-
-
-
-sample.list <- readWorksheetFromFile("AAs-HPLC-test-2018_02_21.xlsx", "Sample info")
-sample.data <- merge(final.summary$Sample, sample.list, by.x = "Sample.name", by.y = "Sample.label.on.tube")
-
-condi.colnames <- c("Condition.1", "Condition.2")
-
-
-### Create a group variable based on sample list (e.g. different species, conditions, treatments, etc.)
-if(length(condi.colnames) > 1)
-
-{sample.data$GroupVar <- apply(sample.data[,condi.colnames], 1, function(x){paste(x, collapse = "\n")})
-}else{
- sample.data$GroupVar <- sample.data[,condi.colnames]
-}
-
-sample.data$GroupVar <- factor(sample.data$GroupVar, levels = unique(sample.data[order(sample.data[,condi.colnames[1]]), "GroupVar"]))
-sample.data$Amount <- as.numeric(sample.data$Amount)
-
-sample.data$µmol.mg.FW <- sample.data$Amount / sample.data$Sample.weight..mg. * 1000
-
-
-p2 <- ggplot(sample.data, aes(x = GroupVar, y = µmol.mg.FW)) +
- geom_point() +
- facet_wrap(~Compound, scales = "free") +
- theme_dominik
-
-
-pdf("02.2AminoAcids.pdf",width = 12, height = 12)
-p2
-dev.off()
-
-
-
-
-
-
-
-
-
-
diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/2018-03-14_EvaReport.pdf b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/2018-03-14_EvaReport.pdf
deleted file mode 100755
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/2018-03-14_EvaReport.xlsx b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/2018-03-14_EvaReport.xlsx
deleted file mode 100755
index 6123fa55e07a9f64883c2f6991e6d35734c31625..0000000000000000000000000000000000000000
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/2018-03-15_01.Data.xlsx b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-03-15_DataAnalysis/2018-03-15_01.Data.xlsx
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-05_DataAnalysis_UpdatedMethod/.DS_Store b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-05_DataAnalysis_UpdatedMethod/.DS_Store
deleted file mode 100755
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-05_DataAnalysis_UpdatedMethod/.Rhistory b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-05_DataAnalysis_UpdatedMethod/.Rhistory
deleted file mode 100755
index a587fee9b2d2ea0c43b1e6817c3ee11ce8a8deb2..0000000000000000000000000000000000000000
--- a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-05_DataAnalysis_UpdatedMethod/.Rhistory
+++ /dev/null
@@ -1,234 +0,0 @@
-setwd("/Volumes/data/MSlab/05_projects/18-0008_Eva_Maleckova/UHPLC-DAD/2018-04-05_DataAnalysis_UpdatedMethod/")
-rm(list = ls())
-library(XLConnect)
-library(openxlsx)
-getSheets(lc.report)
-?read.xlsx
-lc.report <- read.xlsx("2018-03-14_EvaReport.xlsx")
-lc.report <- read.xlsx("2018-04-05_Report.xlsx")
-library(readxl)
-install.packages(readxl)
-install.packages('readxl')
-library(readxl)
-library(readxl)
-lc.report <- "2018-04-05_Report.xlsx"
-excel_sheets(lc.report)
-report.summmary <- list()
-for(i in excel_sheets(lc.report))
-{
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-type <- info2$b[3]
-sample.data <- current.sheet[14:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]
-if(type == "Calibration"){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1,]
-colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-}
-i
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-type <- info2$b[3]
-type
-info
-current.sheet
-info1
-info2
-current.sheet
-info1
-info <- t(rbind(info1, info2, info3))
-info
-type
-if(type == "Calibration"){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-if(type == "Calibration" & !is.na(type)){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1,]
-sample.data
-sample.data <- sample.data[-1,]
-colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-report.summmary
-{
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-type <- info2$b[3]
-sample.data <- current.sheet[14:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]
-if(type == "Calibration" & !is.na(type)){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1,]
-colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-}
-report.summmary <- list()
-for(i in excel_sheets(lc.report))
-{
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-type <- info2$b[3]
-sample.data <- current.sheet[14:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]
-if(type == "Calibration" & !is.na(type)){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1,]
-colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-}
-report.summmary
-excel_sheets(lc.report)
-i <- "Page 2"
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-info3
-info2
-current.sheet
-View(current.sheet)
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(10, 13)]
-View(current.sheet)
-info3 <- current.sheet[13, c(1, 3)]
-info3
-View(current.sheet)
-View(current.sheet)
-info3 <- current.sheet[12, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-info
-type <- info2$b[3]
-type
-if(type == "Calibration"){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-sample.data
-report.summmary <- list()
-for(i in excel_sheets(lc.report))
-{
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(10, 13)]
-info3 <- current.sheet[12, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-type <- info2$b[3]
-sample.data <- current.sheet[14:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]
-if(type == "Calibration"){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1,]
-colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-}
-i
-report.summmary$Calibration
-report.summmary$Sample
-final.summary <- list()
-for(type in names(report.summmary))
-{
-final.summary[[type]] <- do.call(rbind, report.summmary[[type]])
-}
-final.summary
-save(final.summary, file = "01.UHPLC.RData")
-setwd("/Volumes/data/MSlab/05_projects/18-0008_Eva_Maleckova/UHPLC-DAD/2018-04-05_DataAnalysis_UpdatedMethod/")
-rm(list = ls())
-required.packages <- c("Rmisc", "plyr", "ggplot2", "readxl","reshape2", "gridExtra")
-for(package in required.packages)
-{
-print(package)
-## Check if package is installed. If not, install
-if(!package %in% row.names(installed.packages())){install.packages(package, repos ="https://cran.uni-muenster.de/")}
-# ## Check if package is up to date. If not, update
-# update.packages(package, repos = "https://cran.uni-muenster.de/")
-## Load package
-library(package, character.only = T)
-}
-theme_dominik <-
-theme(panel.background = element_blank(), panel.border = element_rect(fill = NA)) +
-theme(axis.text = element_text(color = "black"), axis.ticks = element_line(color = "black"), axis.title = element_text(color = "black")) +
-theme(plot.title = element_text(face= "bold")) +
-theme(aspect.ratio = 1) +
-theme(strip.background = element_blank(), strip.text = element_text(size = 10, face = "bold")) +
-theme(legend.position = "bottom", legend.direction = "horizontal", legend.title = element_blank())
-ggplotRegression <- function (fit) {
-ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
-stat_smooth(method = "lm", col = "firebrick") +
-geom_point(size = 2) +
-annotate("text", x = min(fit$model[,2]), y = max(fit$model[,1]), hjust = 0, vjust = 1, label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
-"\nIntercept =",signif(fit$coef[[1]],2 ),
-"\nSlope =",signif(fit$coef[[2]], 2),
-"\nP =",signif(summary(fit)$coef[2,4], 2))
-) +
-theme_dominik
-}
-load("01.UHPLC.RData")
-calib <- final.summary$Calibration
-calib$std.amount <- as.numeric(do.call(rbind, strsplit(calib$Sample.name, split = " "))[,1])
-calib <- subset(calib, !is.na(Amount))
-calib <- subset(calib, Sample.name != "200 pmol Mix")
-calib <- subset(calib, Compound != "Histidine")
-count(calib$Compound)
-calib <- final.summary$Calibration
-calib
diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-05_DataAnalysis_UpdatedMethod/01.UHPLC.RData b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-05_DataAnalysis_UpdatedMethod/01.UHPLC.RData
deleted file mode 100755
index 525bfc0b3f456219de96bba2911331a635551414..0000000000000000000000000000000000000000
Binary files a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-05_DataAnalysis_UpdatedMethod/01.UHPLC.RData and /dev/null differ
diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-05_DataAnalysis_UpdatedMethod/01UHPLC-DAD_Scram.R b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-05_DataAnalysis_UpdatedMethod/01UHPLC-DAD_Scram.R
deleted file mode 100755
index cb7f7a52e288d9e2bae886fa05d1d5af82a48569..0000000000000000000000000000000000000000
--- a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-05_DataAnalysis_UpdatedMethod/01UHPLC-DAD_Scram.R
+++ /dev/null
@@ -1,91 +0,0 @@
-
-
-
-setwd("/Volumes/data/MSlab/21_projects/18-0008_Eva_Maleckova/UHPLC-DAD/2018-04-05_DataAnalysis_UpdatedMethod/")
-rm(list = ls())
-
-library(readxl)
-
-lc.report <- "2018-04-05_Report.xlsx"
-
-
-report.summmary <- list()
-for(i in excel_sheets(lc.report))
-{
-
- current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-
- info1 <- current.sheet[1:6, c(2, 5)]
- info2 <- current.sheet[3:5, c(10, 13)]
- info3 <- current.sheet[12, c(1, 3)]
-
- colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-
- info <- t(rbind(info1, info2, info3))
-
- type <- info2$b[3]
-
- sample.data <- current.sheet[14:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]
-
- if(type == "Calibration"){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-
- colnames(sample.data) <- sample.data[1,]
- sample.data <- sample.data[-1,]
-
- colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-
- sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-
- duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
- colnames(duplicated.info) <- gsub(":", "", info[1,])
- for(j in 1:nrow(sample.data))
- {
- duplicated.info <- rbind(duplicated.info, info[2,])
- }
- duplicated.info <- duplicated.info[-1,]
-
-
- all.data <- cbind.data.frame(duplicated.info, sample.data)
- colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-
- report.summmary[[type]][[i]] <- all.data
-
-}
-
-
-final.summary <- list()
-for(type in names(report.summmary))
-{
- final.summary[[type]] <- do.call(rbind, report.summmary[[type]])
-}
-
-#
-#
-# ############################
-# #### Export data
-# xlcFreeMemory()
-#
-#
-# Data.xlsx <- loadWorkbook(paste(Sys.Date(), "01.Data.xlsx", sep = "_"), create = TRUE)
-#
-# createSheet(Data.xlsx, "SampleData")
-# writeWorksheet(Data.xlsx, final.summary$Sample, "SampleData")
-# saveWorkbook(Data.xlsx)
-#
-# createSheet(Data.xlsx, "Calibration")
-# writeWorksheet(Data.xlsx, final.summary$Calibration, "Calibration")
-# saveWorkbook(Data.xlsx)
-#
-# createSheet(Data.xlsx, "Blank")
-# writeWorksheet(Data.xlsx, final.summary$Blank, "Blank")
-# saveWorkbook(Data.xlsx)
-
-
-
-
-save(final.summary, file = "01.UHPLC.RData")
-
-
-
-
-
diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-05_DataAnalysis_UpdatedMethod/02UHPLC.Analysis.R b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-05_DataAnalysis_UpdatedMethod/02UHPLC.Analysis.R
deleted file mode 100755
index dabc49fd4582fb7295a3d5a544634c7ef498dfd4..0000000000000000000000000000000000000000
--- a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-05_DataAnalysis_UpdatedMethod/02UHPLC.Analysis.R
+++ /dev/null
@@ -1,124 +0,0 @@
-
-
-setwd("/Volumes/data/MSlab/21_projects/18-0008_Eva_Maleckova/UHPLC-DAD/2018-04-05_DataAnalysis_UpdatedMethod/")
-rm(list = ls())
-
-
-#################################################
-
-required.packages <- c("Rmisc", "plyr", "ggplot2", "readxl","reshape2", "gridExtra")
-
-for(package in required.packages)
-{
- print(package)
- ## Check if package is installed. If not, install
- if(!package %in% row.names(installed.packages())){install.packages(package, repos ="https://cran.uni-muenster.de/")}
- # ## Check if package is up to date. If not, update
- # update.packages(package, repos = "https://cran.uni-muenster.de/")
- ## Load package
- library(package, character.only = T)
-}
-
-
-theme_dominik <-
- theme(panel.background = element_blank(), panel.border = element_rect(fill = NA)) +
- theme(axis.text = element_text(color = "black"), axis.ticks = element_line(color = "black"), axis.title = element_text(color = "black")) +
- theme(plot.title = element_text(face= "bold")) +
- theme(aspect.ratio = 1) +
- theme(strip.background = element_blank(), strip.text = element_text(size = 10, face = "bold")) +
- theme(legend.position = "bottom", legend.direction = "horizontal", legend.title = element_blank())
-
-ggplotRegression <- function (fit) {
-
- ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
- stat_smooth(method = "lm", col = "firebrick") +
- geom_point(size = 2) +
- annotate("text", x = min(fit$model[,2]), y = max(fit$model[,1]), hjust = 0, vjust = 1, label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
- "\nIntercept =",signif(fit$coef[[1]],2 ),
- "\nSlope =",signif(fit$coef[[2]], 2),
- "\nP =",signif(summary(fit)$coef[2,4], 2))
- ) +
- theme_dominik
-}
-
-
-
-
-load("01.UHPLC.RData")
-
-
-### Calibration curves
-
-
-calib <- final.summary$Calibration
-calib$std.amount <- as.numeric(do.call(rbind, strsplit(calib$Sample.name, split = " "))[,1])
-
-calib <- subset(calib, !is.na(Amount))
-calib <- subset(calib, Sample.name != "200 pmol Mix")
-
-calib <- subset(calib, Compound != "Histidine")
-
-count(calib$Compound)
-
-calib.list <- list()
-for(cc in unique(calib$Compound))
-{
- calib.list[[cc]] <- ggplotRegression(lm(std.amount ~ Amount, data = subset(calib, Compound == cc))) + ggtitle(cc)
-}
-
-
-
-# p1 <- ggplot(calib, aes(x = std.amount, y = Amount)) +
- # geom_point() +
- # facet_wrap(~Compound) +
- # theme_dominik + theme(panel.grid.major = element_line(colour = "grey"))
-
-
-pdf("02.1CalibrationCurves.pdf",width = 20, height = 20)
-do.call(grid.arrange, calib.list)
-dev.off()
-
-
-
-
-
-
-sample.list <- readWorksheetFromFile("AAs-HPLC-test-2018_02_21.xlsx", "Sample info")
-sample.data <- merge(final.summary$Sample, sample.list, by.x = "Sample.name", by.y = "Sample.label.on.tube")
-
-condi.colnames <- c("Condition.1", "Condition.2")
-
-
-### Create a group variable based on sample list (e.g. different species, conditions, treatments, etc.)
-if(length(condi.colnames) > 1)
-
-{sample.data$GroupVar <- apply(sample.data[,condi.colnames], 1, function(x){paste(x, collapse = "\n")})
-}else{
- sample.data$GroupVar <- sample.data[,condi.colnames]
-}
-
-sample.data$GroupVar <- factor(sample.data$GroupVar, levels = unique(sample.data[order(sample.data[,condi.colnames[1]]), "GroupVar"]))
-sample.data$Amount <- as.numeric(sample.data$Amount)
-
-sample.data$µmol.mg.FW <- sample.data$Amount / sample.data$Sample.weight..mg. * 1000
-
-
-p2 <- ggplot(sample.data, aes(x = GroupVar, y = µmol.mg.FW)) +
- geom_point() +
- facet_wrap(~Compound, scales = "free") +
- theme_dominik
-
-
-pdf("02.2AminoAcids.pdf",width = 12, height = 12)
-p2
-dev.off()
-
-
-
-
-
-
-
-
-
-
diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/.Rhistory b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/.Rhistory
deleted file mode 100755
index a587fee9b2d2ea0c43b1e6817c3ee11ce8a8deb2..0000000000000000000000000000000000000000
--- a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/.Rhistory
+++ /dev/null
@@ -1,234 +0,0 @@
-setwd("/Volumes/data/MSlab/05_projects/18-0008_Eva_Maleckova/UHPLC-DAD/2018-04-05_DataAnalysis_UpdatedMethod/")
-rm(list = ls())
-library(XLConnect)
-library(openxlsx)
-getSheets(lc.report)
-?read.xlsx
-lc.report <- read.xlsx("2018-03-14_EvaReport.xlsx")
-lc.report <- read.xlsx("2018-04-05_Report.xlsx")
-library(readxl)
-install.packages(readxl)
-install.packages('readxl')
-library(readxl)
-library(readxl)
-lc.report <- "2018-04-05_Report.xlsx"
-excel_sheets(lc.report)
-report.summmary <- list()
-for(i in excel_sheets(lc.report))
-{
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-type <- info2$b[3]
-sample.data <- current.sheet[14:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]
-if(type == "Calibration"){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1,]
-colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-}
-i
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-type <- info2$b[3]
-type
-info
-current.sheet
-info1
-info2
-current.sheet
-info1
-info <- t(rbind(info1, info2, info3))
-info
-type
-if(type == "Calibration"){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-if(type == "Calibration" & !is.na(type)){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1,]
-sample.data
-sample.data <- sample.data[-1,]
-colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-report.summmary
-{
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-type <- info2$b[3]
-sample.data <- current.sheet[14:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]
-if(type == "Calibration" & !is.na(type)){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1,]
-colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-}
-report.summmary <- list()
-for(i in excel_sheets(lc.report))
-{
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-type <- info2$b[3]
-sample.data <- current.sheet[14:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]
-if(type == "Calibration" & !is.na(type)){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1,]
-colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-}
-report.summmary
-excel_sheets(lc.report)
-i <- "Page 2"
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(9, 11)]
-info3 <- current.sheet[13, c(1, 3)]
-info3
-info2
-current.sheet
-View(current.sheet)
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(10, 13)]
-View(current.sheet)
-info3 <- current.sheet[13, c(1, 3)]
-info3
-View(current.sheet)
-View(current.sheet)
-info3 <- current.sheet[12, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-info
-type <- info2$b[3]
-type
-if(type == "Calibration"){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-sample.data
-report.summmary <- list()
-for(i in excel_sheets(lc.report))
-{
-current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-info1 <- current.sheet[1:6, c(2, 5)]
-info2 <- current.sheet[3:5, c(10, 13)]
-info3 <- current.sheet[12, c(1, 3)]
-colnames(info1) <- colnames(info2) <- colnames(info3) <- c("a", "b")
-info <- t(rbind(info1, info2, info3))
-type <- info2$b[3]
-sample.data <- current.sheet[14:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]
-if(type == "Calibration"){sample.data <- current.sheet[13:(nrow(current.sheet)-1), c(1, 4, 6, 7, 8, 10)]}
-colnames(sample.data) <- sample.data[1,]
-sample.data <- sample.data[-1,]
-colnames(sample.data)[c(1, 5:6)] <- c("Compound", "Amount", "Concentration")
-sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
-colnames(duplicated.info) <- gsub(":", "", info[1,])
-for(j in 1:nrow(sample.data))
-{
-duplicated.info <- rbind(duplicated.info, info[2,])
-}
-duplicated.info <- duplicated.info[-1,]
-all.data <- cbind.data.frame(duplicated.info, sample.data)
-colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-report.summmary[[type]][[i]] <- all.data
-}
-i
-report.summmary$Calibration
-report.summmary$Sample
-final.summary <- list()
-for(type in names(report.summmary))
-{
-final.summary[[type]] <- do.call(rbind, report.summmary[[type]])
-}
-final.summary
-save(final.summary, file = "01.UHPLC.RData")
-setwd("/Volumes/data/MSlab/05_projects/18-0008_Eva_Maleckova/UHPLC-DAD/2018-04-05_DataAnalysis_UpdatedMethod/")
-rm(list = ls())
-required.packages <- c("Rmisc", "plyr", "ggplot2", "readxl","reshape2", "gridExtra")
-for(package in required.packages)
-{
-print(package)
-## Check if package is installed. If not, install
-if(!package %in% row.names(installed.packages())){install.packages(package, repos ="https://cran.uni-muenster.de/")}
-# ## Check if package is up to date. If not, update
-# update.packages(package, repos = "https://cran.uni-muenster.de/")
-## Load package
-library(package, character.only = T)
-}
-theme_dominik <-
-theme(panel.background = element_blank(), panel.border = element_rect(fill = NA)) +
-theme(axis.text = element_text(color = "black"), axis.ticks = element_line(color = "black"), axis.title = element_text(color = "black")) +
-theme(plot.title = element_text(face= "bold")) +
-theme(aspect.ratio = 1) +
-theme(strip.background = element_blank(), strip.text = element_text(size = 10, face = "bold")) +
-theme(legend.position = "bottom", legend.direction = "horizontal", legend.title = element_blank())
-ggplotRegression <- function (fit) {
-ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
-stat_smooth(method = "lm", col = "firebrick") +
-geom_point(size = 2) +
-annotate("text", x = min(fit$model[,2]), y = max(fit$model[,1]), hjust = 0, vjust = 1, label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
-"\nIntercept =",signif(fit$coef[[1]],2 ),
-"\nSlope =",signif(fit$coef[[2]], 2),
-"\nP =",signif(summary(fit)$coef[2,4], 2))
-) +
-theme_dominik
-}
-load("01.UHPLC.RData")
-calib <- final.summary$Calibration
-calib$std.amount <- as.numeric(do.call(rbind, strsplit(calib$Sample.name, split = " "))[,1])
-calib <- subset(calib, !is.na(Amount))
-calib <- subset(calib, Sample.name != "200 pmol Mix")
-calib <- subset(calib, Compound != "Histidine")
-count(calib$Compound)
-calib <- final.summary$Calibration
-calib
diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/01.UHPLC.RData b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/01.UHPLC.RData
deleted file mode 100755
index a58aacbcca6a51755739db890777c5fd070e4010..0000000000000000000000000000000000000000
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/01UHPLC-DAD_Scram.R b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/01UHPLC-DAD_Scram.R
deleted file mode 100755
index e1d1ba2d692ea1112aabc0830991b14f286fecf1..0000000000000000000000000000000000000000
--- a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/01UHPLC-DAD_Scram.R
+++ /dev/null
@@ -1,84 +0,0 @@
-
-
-
-setwd("/Volumes/data/MSlab/21_projects/18-0008_Eva_Maleckova/UHPLC-DAD/2018-04-11_DataAnalysis_UpUpdated/")
-rm(list = ls())
-
-library(readxl)
-
-lc.report <- "2018-04-10_Report.xlsx"
-
-
-report.summmary <- list()
-for(i in excel_sheets(lc.report))
-{
-
- current.sheet <- as.data.frame(read_xlsx(lc.report, sheet = i, col_names = F))
-
- if(!current.sheet[1, 2] %in% c("Blank", "blank"))
- {
-
-
- info.table <- c()
- for(row in 1:(which(current.sheet[, 1] == 'Name')-1) )
- {
-
- x <- current.sheet[row, 1:5]
- y <- x[!is.na(x)]
- if(length(y) == 2){info.table <- c(info.table, y)}
- if(length(y) == 1){info.table <- c(info.table, c(y, 'NA'))}
-
- x <- current.sheet[row, 6:ncol(current.sheet)]
- y <- x[!is.na(x)]
- if(length(y) == 2){info.table <- c(info.table, y)}
- if(length(y) == 1){info.table <- c(info.table, c(y, 'NA'))}
-
- }
-
- info <- t(data.frame('a' = info.table[seq(1, length(info.table), 2)], 'b' = info.table[seq(2, length(info.table), 2)]))
-
- type <- info['b', 8]
-
- sample.data <- current.sheet[which(current.sheet[, 1] == 'Name'):(nrow(current.sheet)-1), ]
- colnames(sample.data) <- sample.data[1,]
- sample.data <- sample.data[-1, !is.na(colnames(sample.data))]
-
- sample.data <- sample.data[, apply(sample.data, 2, function(x){sum(is.na(x)) != nrow(sample.data)})]
-
- colnames(sample.data)[c(1, 5, 6)] <- c("Compound", "Amount_pmol", "Concentration_pmol.µl")
-
- sample.data[,2:6] <- apply(sample.data[,2:6], 2, function(x){as.numeric(x)})
-
- duplicated.info <- data.frame(matrix(NA, ncol = ncol(info)))
- colnames(duplicated.info) <- gsub(":", "", info[1,])
- for(j in 1:nrow(sample.data))
- {
- duplicated.info <- rbind(duplicated.info, info[2,])
- }
- duplicated.info <- duplicated.info[-1,]
-
- all.data <- cbind.data.frame(duplicated.info, sample.data)
- colnames(all.data) <- gsub(" ", ".", colnames(all.data))
-
- report.summmary[[type]][[i]] <- all.data
-
- }
-
-}
-
-
-final.summary <- list()
-for(type in names(report.summmary))
-{
- final.summary[[type]] <- do.call(rbind, report.summmary[[type]])
-
-
-}
-
-
-save(final.summary, file = "01.UHPLC.RData")
-
-
-
-
-
diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/02UHPLC.Analysis.R b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/02UHPLC.Analysis.R
deleted file mode 100755
index 143f9f688c0859ee20f0c428366d4eaf7f470555..0000000000000000000000000000000000000000
--- a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/02UHPLC.Analysis.R
+++ /dev/null
@@ -1,166 +0,0 @@
-
-
-setwd("/Volumes/data/MSlab/21_projects/18-0008_Eva_Maleckova/UHPLC-DAD/2018-04-11_DataAnalysis_UpUpdated/")
-rm(list = ls())
-
-
-sample.list <- data.frame(read_xlsx("../AAs-HPLC-test-2018_02_21_DB.xlsx", "Sample list"))
-condi.colnames <- c("Condition.1", "Condition.2")
-matching.name.col <- 'Sample.ID'
-
-#################################################
-
-required.packages <- c("Rmisc", "plyr", "ggplot2", "readxl","reshape2", "gridExtra")
-
-for(package in required.packages)
-{
- print(package)
- ## Check if package is installed. If not, install
- if(!package %in% row.names(installed.packages())){install.packages(package, repos ="https://cran.uni-muenster.de/")}
- # ## Check if package is up to date. If not, update
- # update.packages(package, repos = "https://cran.uni-muenster.de/")
- ## Load package
- library(package, character.only = T)
-}
-
-
-theme_dominik <-
- theme(panel.background = element_blank(), panel.border = element_rect(fill = NA)) +
- theme(axis.text = element_text(color = "black"), axis.ticks = element_line(color = "black"), axis.title.y = element_text(color = "black"), axis.title.x = element_blank()) +
- theme(plot.title = element_text(face= "bold")) +
- theme(aspect.ratio = 1) +
- theme(strip.background = element_blank(), strip.text = element_text(size = 10, face = "bold")) +
- theme(legend.position = "right", legend.direction = "vertical", legend.title = element_blank())
-
-ggplotRegression <- function (fit) {
-
- ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) +
- stat_smooth(method = "lm", col = "firebrick") +
- geom_point(size = 2) +
- annotate("text", x = min(fit$model[,2]), y = max(fit$model[,1]), hjust = 0, vjust = 1, label = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 4),
- "\nIntercept =",signif(fit$coef[[1]],2 ),
- "\nSlope =",signif(fit$coef[[2]], 2),
- "\nP =",signif(summary(fit)$coef[2,4], 2))
- ) +
- theme_dominik
-}
-
-
-
-
-load("01.UHPLC.RData")
-
-
-### Calibration curves
-
-
-calib <- final.summary$Calibration
-calib$std.amount <- as.numeric(gsub('NA', '', do.call(rbind, lapply(strsplit(calib$Sample.name, split = ""), function(x){paste(as.numeric(x), collapse = '')}))))
-
-# calib <- subset(calib, !is.na(Amount[pmol]))
-# calib <- subset(calib, Sample.name != "200 pmol Mix")
-
-calib <- subset(calib, !Compound %in% c('Histidine', 'Tryptophane', 'Norvaline'))
-
-count(calib$Compound)
-
-calib.list <- list()
-for(cc in unique(calib$Compound))
-{
- calib.list[[cc]] <- ggplotRegression(lm(Concentration_pmol.µl ~ std.amount, data = subset(calib, Compound == cc))) + ggtitle(cc)
-}
-
-
-
-# p1 <- ggplot(calib, aes(x = std.amount, y = Amount)) +
- # geom_point() +
- # facet_wrap(~Compound) +
- # theme_dominik + theme(panel.grid.major = element_line(colour = "grey"))
-
-
-pdf(paste(Sys.Date(), "CalibrationCurves.pdf", sep = ''),width = 20, height = 20)
-do.call(grid.arrange, calib.list)
-dev.off()
-
-
-
-
-sample.data <- merge(final.summary$Sample, sample.list, by.x = "Sample.name", by.y = matching.name.col)
-
-sample.data <- subset(sample.data, Compound != 'Norvaline')
-
-
-### Create a group variable based on sample list (e.g. different species, conditions, treatments, etc.)
-if(length(condi.colnames) > 1)
-
-{sample.data$GroupVar <- apply(sample.data[,condi.colnames], 1, function(x){paste(x, collapse = "\n")})
-}else{
- sample.data$GroupVar <- sample.data[,condi.colnames]
-}
-
-sample.data$GroupVar <- factor(sample.data$GroupVar, levels = unique(sample.data[order(sample.data[,condi.colnames[1]], sample.data[,condi.colnames[2]]), "GroupVar"]))
-
-sample.data$Inj..volume <- as.numeric(sample.data$Inj..volume)
-
-
-
-if(length(unique(as.numeric(c(sample.data$Inj..volume, calib$Inj..volume)))) != 1){warning("Injection volume was not the same across all measurements")}
-
-
-# sample.data$AmountInDeriv <- sample.data$Amount / sample.data$Total.derivatisation..volume..µl. * sample.data$Inj..volume
-# sample.data$AmountInResusp <- sample.data$AmountInDeriv * sample.data$Resuspension...volume....µl. / sample.data$Sample.volume...used.for.derivatisation..µl.
-# # sample.data$AmountInExtract <- sample.data$AmountInResusp * sample.data$Extraction...volume...µl. / sample.data$Volume.in...speed.vac....µl.
-# # sample.data$pmol.mg.FW <- sample.data$AmountInExtract / sample.data$Fresh.weight..mg..or...culture.volume..ml....used.for.extraction
-# sample.data$pmol.mg.FW <- sample.data$AmountInExtract / sample.data$OD
-#
-
-
-## Calculate the amount (in pmol) in the derivatization
-## 1µl is injected out of e.g. 50 µl derivatization mix
-## e.g. 15 pmol/µl * 1 µl injected * 50 µl (total) / 1 µl (inj)
-
-sample.data$AmountInDeriv <- sample.data$Concentration_pmol.µl * sample.data$Total.derivatisation..volume..µl.
-
-## Only a fraction (typically 1/5) of the speed vac reuspension is used
-sample.data$AmountInResusp <- sample.data$AmountInDeriv * sample.data$Resuspension...volume....µl. / sample.data$Sample.volume...used.for.derivatisation..µl.
-
-## During speed vac, the sample is concentrated (e.g. 4x)
-sample.data$AmountInSpeedVac <- sample.data$AmountInResusp * sample.data$Resuspension...volume....µl. / sample.data$Volume.in...speed.vac....µl.
-
-## Only a fraction (typically 1/4) of the extract is used
-sample.data$AmountInExtract <- sample.data$AmountInSpeedVac * sample.data$Extraction...volume...µl. / sample.data$Volume.in...speed.vac....µl.
-
-## Normalize for mg FW
-sample.data$pmol.mg <- sample.data$AmountInExtract / sample.data$Fresh.weight..mg..or...culture.volume..ml....used.for.extraction
-sample.data$nmol.mg <- sample.data$pmol.mg / 1000
-
-## Normalize for culture volume and OD
-# sample.data$pmol.ml.OD <- sample.data$AmountInExtract / sample.data$Fresh.weight..mg..or...culture.volume..ml....used.for.extraction / sample.data$Cultured..density...OD.
-# sample.data$nmol.ml.OD <- sample.data$pmol.ml.OD / 1000
-
-
-
-# p2 <- ggplot(sample.data, aes(x = GroupVar, y = nmol.ml.OD)) +
-p2 <- ggplot(sample.data, aes(x = GroupVar, y = nmol.mg)) +
- # geom_point(aes(col = Condition.2, shape = Condition.3)) +
- geom_text(aes(label = Sample.name, col = GroupVar), size = 2) +
- facet_wrap(~Compound, scales = "free") +
- # scale_color_brewer() +
- theme_dominik +
- theme(axis.text.x = element_blank())
-
-
-pdf(paste(Sys.Date(), "AminoAcids.pdf", sep = ''),width = 16, height = 16)
-p2
-dev.off()
-
-
-
-write.table(sample.data, file = paste(Sys.Date(), 'Data.txt', sep = ''), sep = '\t', row.names = F)
-
-
-
-
-sample.data$GroupVar
-
-
diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/2018-04-10_Report.pdf b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/2018-04-10_Report.pdf
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/2018-04-10_Report.xlsx b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/2018-04-10_Report.xlsx
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/2018-04-12AminoAcids.pdf b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/2018-04-12AminoAcids.pdf
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/2018-04-12CalibrationCurves.pdf b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/2018-04-12CalibrationCurves.pdf
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diff --git a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/2018-04-12Data.txt b/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/2018-04-12Data.txt
deleted file mode 100755
index 32b82a64cbea32ba9c2428c741528f1849a552f8..0000000000000000000000000000000000000000
--- a/cmml/18-0008_Eva_Maleckova/UHPLC-DAD_testRun/2018-04-11_DataAnalysis_UpUpdated/2018-04-12Data.txt
+++ /dev/null
@@ -1,273 +0,0 @@
-"Sample.name" "Data.file" "Instrument" "Injection.date" "Inj..volume" "Location" "Acq..method" "Type" "Processing.method" "Manually.modified" "Signal" "Compound" "RT.[min]" "RF" "Area" "Amount_pmol" "Concentration_pmol.µl" "ISTD.Name" "Sample.number" "Species" "Tissue.type" "Condition.1" "Condition.2" "Condition.3" "Technical.replicate" "Biological.replicate" "Cultured..density...OD." "Fresh.weight..mg..or...culture.volume..ml....used.for.extraction" "Extraction..buffer" "Extraction...volume...µl." "Volume.in...speed.vac....µl." "Resuspension...volume....µl." "Sample.volume...used.for.derivatisation..µl." "Total.derivatisation..volume..µl." "GroupVar" "AmountInDeriv" "AmountInResusp" "AmountInSpeedVac" "AmountInExtract" "pmol.mg" "nmol.mg"
-"102.1" "180301_10.dx" "OpenLab 1" "2018-03-01 18:08:21+01:00" 1 "P1-B-4" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Serine" 2.022 0.369 18.806 3.14 3.14 "Norvaline" 4 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 1 1 "NA" 42.8 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 157 785 392.5 4710 110.046728971963 0.110046728971963
-"102.1" "180301_10.dx" "OpenLab 1" "2018-03-01 18:08:21+01:00" 1 "P1-B-4" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Arginine + Glutamine" 2.079 0.314 16.264 3.186 3.186 "Norvaline" 4 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 1 1 "NA" 42.8 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 159.3 796.5 398.25 4779 111.658878504673 0.111658878504673
-"102.1" "180301_10.dx" "OpenLab 1" "2018-03-01 18:08:21+01:00" 1 "P1-B-4" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glycine" 2.25 0.4 6.463 0.995 0.995 "Norvaline" 4 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 1 1 "NA" 42.8 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 49.75 248.75 124.375 1492.5 34.8714953271028 0.0348714953271028
-"102.1" "180301_10.dx" "OpenLab 1" "2018-03-01 18:08:21+01:00" 1 "P1-B-4" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Aspartate" 2.4 0.388 13.701 2.174 2.174 "Norvaline" 4 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 1 1 "NA" 42.8 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 108.7 543.5 271.75 3261 76.1915887850467 0.0761915887850467
-"102.1" "180301_10.dx" "OpenLab 1" "2018-03-01 18:08:21+01:00" 1 "P1-B-4" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glutamate" 2.782 0.217 78.192 22.189 22.189 "Norvaline" 4 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 1 1 "NA" 42.8 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 1109.45 5547.25 2773.625 33283.5 777.651869158879 0.777651869158879
-"102.1" "180301_10.dx" "OpenLab 1" "2018-03-01 18:08:21+01:00" 1 "P1-B-4" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Threonine" 3.176 -0.006 0.128 -1.426 -1.426 "Norvaline" 4 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 1 1 "NA" 42.8 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -71.3 -356.5 -178.25 -2139 -49.9766355140187 -0.0499766355140187
-"102.1" "180301_10.dx" "OpenLab 1" "2018-03-01 18:08:21+01:00" 1 "P1-B-4" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Alanine" 3.602 -1.074 3.687 -0.212 -0.212 "Norvaline" 4 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 1 1 "NA" 42.8 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -10.6 -53 -26.5 -318 -7.42990654205608 -0.00742990654205608
-"102.1" "180301_10.dx" "OpenLab 1" "2018-03-01 18:08:21+01:00" 1 "P1-B-4" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Proline" 4.325 0.827 4.124 0.307 0.307 "Norvaline" 4 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 1 1 "NA" 42.8 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 15.35 76.75 38.375 460.5 10.7593457943925 0.0107593457943925
-"102.1" "180301_10.dx" "OpenLab 1" "2018-03-01 18:08:21+01:00" 1 "P1-B-4" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Lysine" 6.077 -0.791 1.152 -0.09 -0.09 "Norvaline" 4 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 1 1 "NA" 42.8 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -4.5 -22.5 -11.25 -135 -3.15420560747664 -0.00315420560747664
-"102.1" "180301_10.dx" "OpenLab 1" "2018-03-01 18:08:21+01:00" 1 "P1-B-4" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Tyrosine" 6.266 -0.197 1.572 -0.491 -0.491 "Norvaline" 4 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 1 1 "NA" 42.8 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -24.55 -122.75 -61.375 -736.5 -17.2079439252336 -0.0172079439252336
-"102.1" "180301_10.dx" "OpenLab 1" "2018-03-01 18:08:21+01:00" 1 "P1-B-4" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Valine" 6.702 -0.182 3.726 -1.263 -1.263 "Norvaline" 4 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 1 1 "NA" 42.8 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -63.15 -315.75 -157.875 -1894.5 -44.2640186915888 -0.0442640186915888
-"102.1" "180301_10.dx" "OpenLab 1" "2018-03-01 18:08:21+01:00" 1 "P1-B-4" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Isoleucine" 7.728 -0.334 3.294 -0.607 -0.607 "Norvaline" 4 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 1 1 "NA" 42.8 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -30.35 -151.75 -75.875 -910.5 -21.2733644859813 -0.0212733644859813
-"102.1" "180301_10.dx" "OpenLab 1" "2018-03-01 18:08:21+01:00" 1 "P1-B-4" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Leucine" 7.824 -0.145 2.425 -1.032 -1.032 "Norvaline" 4 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 1 1 "NA" 42.8 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -51.6 -258 -129 -1548 -36.1682242990654 -0.0361682242990654
-"102.1" "180301_10.dx" "OpenLab 1" "2018-03-01 18:08:21+01:00" 1 "P1-B-4" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Phenylalanine" 7.911 -0.072 1.924 -1.65 -1.65 "Norvaline" 4 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 1 1 "NA" 42.8 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -82.5 -412.5 -206.25 -2475 -57.8271028037383 -0.0578271028037383
-"102.2" "180301_11.dx" "OpenLab 1" "2018-03-01 18:18:16+01:00" 1 "P1-B-5" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Serine" 2.016 0.313 20.527 4.74 4.74 "Norvaline" 5 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 2 1 "NA" 47.1 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 237 1185 592.5 7110 150.955414012739 0.150955414012739
-"102.2" "180301_11.dx" "OpenLab 1" "2018-03-01 18:18:16+01:00" 1 "P1-B-5" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Arginine + Glutamine" 2.072 0.303 15.007 3.583 3.583 "Norvaline" 5 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 2 1 "NA" 47.1 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 179.15 895.75 447.875 5374.5 114.108280254777 0.114108280254777
-"102.2" "180301_11.dx" "OpenLab 1" "2018-03-01 18:18:16+01:00" 1 "P1-B-5" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glycine" 2.249 0.303 8.275 1.972 1.972 "Norvaline" 5 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 2 1 "NA" 47.1 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 98.6 493 246.5 2958 62.8025477707006 0.0628025477707006
-"102.2" "180301_11.dx" "OpenLab 1" "2018-03-01 18:18:16+01:00" 1 "P1-B-5" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Aspartate" 2.397 0.261 22.958 6.366 6.366 "Norvaline" 5 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 2 1 "NA" 47.1 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 318.3 1591.5 795.75 9549 202.738853503185 0.202738853503185
-"102.2" "180301_11.dx" "OpenLab 1" "2018-03-01 18:18:16+01:00" 1 "P1-B-5" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glutamate" 2.781 0.212 92.931 31.633 31.633 "Norvaline" 5 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 2 1 "NA" 47.1 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 1581.65 7908.25 3954.125 47449.5 1007.42038216561 1.0074203821656
-"102.2" "180301_11.dx" "OpenLab 1" "2018-03-01 18:18:16+01:00" 1 "P1-B-5" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Alanine" 3.604 -2.575 3.482 -0.098 -0.098 "Norvaline" 5 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 2 1 "NA" 47.1 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -4.9 -24.5 -12.25 -147 -3.12101910828026 -0.00312101910828026
-"102.2" "180301_11.dx" "OpenLab 1" "2018-03-01 18:18:16+01:00" 1 "P1-B-5" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Proline" 4.325 0.35 6.137 1.266 1.266 "Norvaline" 5 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 2 1 "NA" 47.1 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 63.3 316.5 158.25 1899 40.3184713375796 0.0403184713375796
-"102.2" "180301_11.dx" "OpenLab 1" "2018-03-01 18:18:16+01:00" 1 "P1-B-5" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Cysteine" 5.983 -0.003 0.027 -0.648 -0.648 "Norvaline" 5 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 2 1 "NA" 47.1 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -32.4 -162 -81 -972 -20.6369426751592 -0.0206369426751592
-"102.2" "180301_11.dx" "OpenLab 1" "2018-03-01 18:18:16+01:00" 1 "P1-B-5" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Lysine" 6.077 6.165 1.301 0.015 0.015 "Norvaline" 5 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 2 1 "NA" 47.1 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 0.75 3.75 1.875 22.5 0.477707006369427 0.000477707006369427
-"102.2" "180301_11.dx" "OpenLab 1" "2018-03-01 18:18:16+01:00" 1 "P1-B-5" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Tyrosine" 6.265 -0.289 1.678 -0.419 -0.419 "Norvaline" 5 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 2 1 "NA" 47.1 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -20.95 -104.75 -52.375 -628.5 -13.343949044586 -0.013343949044586
-"102.2" "180301_11.dx" "OpenLab 1" "2018-03-01 18:18:16+01:00" 1 "P1-B-5" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Methionine" 6.394 -0.001 0.022 -2.792 -2.792 "Norvaline" 5 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 2 1 "NA" 47.1 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -139.6 -698 -349 -4188 -88.9171974522293 -0.0889171974522293
-"102.2" "180301_11.dx" "OpenLab 1" "2018-03-01 18:18:16+01:00" 1 "P1-B-5" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Valine" 6.702 -0.283 3.958 -1.01 -1.01 "Norvaline" 5 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 2 1 "NA" 47.1 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -50.5 -252.5 -126.25 -1515 -32.1656050955414 -0.0321656050955414
-"102.2" "180301_11.dx" "OpenLab 1" "2018-03-01 18:18:16+01:00" 1 "P1-B-5" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Isoleucine" 7.727 -0.71 3.535 -0.36 -0.36 "Norvaline" 5 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 2 1 "NA" 47.1 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -18 -90 -45 -540 -11.4649681528662 -0.0114649681528662
-"102.2" "180301_11.dx" "OpenLab 1" "2018-03-01 18:18:16+01:00" 1 "P1-B-5" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Leucine" 7.822 -0.223 2.605 -0.843 -0.843 "Norvaline" 5 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 2 1 "NA" 47.1 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -42.15 -210.75 -105.375 -1264.5 -26.8471337579618 -0.0268471337579618
-"102.2" "180301_11.dx" "OpenLab 1" "2018-03-01 18:18:16+01:00" 1 "P1-B-5" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Phenylalanine" 7.91 -0.103 2.121 -1.488 -1.488 "Norvaline" 5 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 2 1 "NA" 47.1 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -74.4 -372 -186 -2232 -47.3885350318471 -0.0473885350318471
-"102.3" "180301_12.dx" "OpenLab 1" "2018-03-01 18:28:10+01:00" 1 "P1-B-6" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Serine" 2.011 0.312 25.508 4.791 4.791 "Norvaline" 6 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 3 1 "NA" 55.3 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 239.55 1197.75 598.875 7186.5 129.9547920434 0.1299547920434
-"102.3" "180301_12.dx" "OpenLab 1" "2018-03-01 18:28:10+01:00" 1 "P1-B-6" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Arginine + Glutamine" 2.068 0.273 24.259 5.2 5.2 "Norvaline" 6 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 3 1 "NA" 55.3 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 260 1300 650 7800 141.048824593128 0.141048824593128
-"102.3" "180301_12.dx" "OpenLab 1" "2018-03-01 18:28:10+01:00" 1 "P1-B-6" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glycine" 2.243 0.316 9.418 1.744 1.744 "Norvaline" 6 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 3 1 "NA" 55.3 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 87.2 436 218 2616 47.3056057866185 0.0473056057866185
-"102.3" "180301_12.dx" "OpenLab 1" "2018-03-01 18:28:10+01:00" 1 "P1-B-6" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Aspartate" 2.392 0.305 19.854 3.812 3.812 "Norvaline" 6 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 3 1 "NA" 55.3 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 190.6 953 476.5 5718 103.399638336347 0.103399638336347
-"102.3" "180301_12.dx" "OpenLab 1" "2018-03-01 18:28:10+01:00" 1 "P1-B-6" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glutamate" 2.775 0.212 114.868 31.688 31.688 "Norvaline" 6 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 3 1 "NA" 55.3 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 1584.4 7922 3961 47532 859.529837251356 0.859529837251356
-"102.3" "180301_12.dx" "OpenLab 1" "2018-03-01 18:28:10+01:00" 1 "P1-B-6" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Threonine" 3.173 -0.013 0.305 -1.38 -1.38 "Norvaline" 6 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 3 1 "NA" 55.3 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -69 -345 -172.5 -2070 -37.4321880650995 -0.0374321880650995
-"102.3" "180301_12.dx" "OpenLab 1" "2018-03-01 18:28:10+01:00" 1 "P1-B-6" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Alanine" 3.599 0.974 5.966 0.358 0.358 "Norvaline" 6 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 3 1 "NA" 55.3 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 17.9 89.5 44.75 537 9.71066907775768 0.00971066907775768
-"102.3" "180301_12.dx" "OpenLab 1" "2018-03-01 18:28:10+01:00" 1 "P1-B-6" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Proline" 4.323 0.33 8.21 1.455 1.455 "Norvaline" 6 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 3 1 "NA" 55.3 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 72.75 363.75 181.875 2182.5 39.4665461121157 0.0394665461121157
-"102.3" "180301_12.dx" "OpenLab 1" "2018-03-01 18:28:10+01:00" 1 "P1-B-6" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Cysteine" 5.976 -0.004 0.047 -0.643 -0.643 "Norvaline" 6 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 3 1 "NA" 55.3 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -32.15 -160.75 -80.375 -964.5 -17.4412296564195 -0.0174412296564195
-"102.3" "180301_12.dx" "OpenLab 1" "2018-03-01 18:28:10+01:00" 1 "P1-B-6" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Lysine" 6.074 5.875 1.609 0.016 0.016 "Norvaline" 6 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 3 1 "NA" 55.3 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" 0.8 4 2 24 0.433996383363472 0.000433996383363472
-"102.3" "180301_12.dx" "OpenLab 1" "2018-03-01 18:28:10+01:00" 1 "P1-B-6" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Tyrosine" 6.262 -0.525 2.73 -0.305 -0.305 "Norvaline" 6 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 3 1 "NA" 55.3 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -15.25 -76.25 -38.125 -457.5 -8.27305605786619 -0.00827305605786618
-"102.3" "180301_12.dx" "OpenLab 1" "2018-03-01 18:28:10+01:00" 1 "P1-B-6" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Valine" 6.699 -0.352 5.344 -0.889 -0.889 "Norvaline" 6 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 3 1 "NA" 55.3 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -44.45 -222.25 -111.125 -1333.5 -24.1139240506329 -0.0241139240506329
-"102.3" "180301_12.dx" "OpenLab 1" "2018-03-01 18:28:10+01:00" 1 "P1-B-6" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Isoleucine" 7.726 -1.17 4.798 -0.24 -0.24 "Norvaline" 6 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 3 1 "NA" 55.3 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -12 -60 -30 -360 -6.50994575045208 -0.00650994575045208
-"102.3" "180301_12.dx" "OpenLab 1" "2018-03-01 18:28:10+01:00" 1 "P1-B-6" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Leucine" 7.822 -0.26 3.449 -0.777 -0.777 "Norvaline" 6 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 3 1 "NA" 55.3 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -38.85 -194.25 -97.125 -1165.5 -21.0759493670886 -0.0210759493670886
-"102.3" "180301_12.dx" "OpenLab 1" "2018-03-01 18:28:10+01:00" 1 "P1-B-6" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Phenylalanine" 7.91 -0.104 2.631 -1.484 -1.484 "Norvaline" 6 "Talinum triangulare" "Leaf" "CAM" "ED" "NA" 3 1 "NA" 55.3 "80% ethanol" 1200 100 50 10 50 "CAM
-ED" -74.2 -371 -185.5 -2226 -40.253164556962 -0.040253164556962
-"122.1" "180301_13.dx" "OpenLab 1" "2018-03-01 18:38:03+01:00" 1 "P1-B-7" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Serine" 2.054 0.245 46.237 12.474 12.474 "Norvaline" 7 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 1 1 "NA" 66.3 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 623.7 3118.5 1559.25 18711 282.217194570136 0.282217194570136
-"122.1" "180301_13.dx" "OpenLab 1" "2018-03-01 18:38:03+01:00" 1 "P1-B-7" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glycine" 2.232 -1.67 2.629 -0.104 -0.104 "Norvaline" 7 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 1 1 "NA" 66.3 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -5.2 -26 -13 -156 -2.35294117647059 -0.00235294117647059
-"122.1" "180301_13.dx" "OpenLab 1" "2018-03-01 18:38:03+01:00" 1 "P1-B-7" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Aspartate" 2.382 0.217 61.876 18.848 18.848 "Norvaline" 7 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 1 1 "NA" 66.3 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 942.4 4712 2356 28272 426.425339366516 0.426425339366516
-"122.1" "180301_13.dx" "OpenLab 1" "2018-03-01 18:38:03+01:00" 1 "P1-B-7" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glutamate" 2.769 0.214 87.353 26.915 26.915 "Norvaline" 7 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 1 1 "NA" 66.3 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 1345.75 6728.75 3364.375 40372.5 608.93665158371 0.60893665158371
-"122.1" "180301_13.dx" "OpenLab 1" "2018-03-01 18:38:03+01:00" 1 "P1-B-7" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Threonine" 3.169 -0.026 0.521 -1.303 -1.303 "Norvaline" 7 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 1 1 "NA" 66.3 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -65.15 -325.75 -162.875 -1954.5 -29.4796380090498 -0.0294796380090498
-"122.1" "180301_13.dx" "OpenLab 1" "2018-03-01 18:38:03+01:00" 1 "P1-B-7" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Alanine" 3.607 -0.029 0.499 -1.118 -1.118 "Norvaline" 7 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 1 1 "NA" 66.3 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -55.9 -279.5 -139.75 -1677 -25.2941176470588 -0.0252941176470588
-"122.1" "180301_13.dx" "OpenLab 1" "2018-03-01 18:38:03+01:00" 1 "P1-B-7" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Proline" 4.32 0.267 11.292 2.795 2.795 "Norvaline" 7 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 1 1 "NA" 66.3 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 139.75 698.75 349.375 4192.5 63.2352941176471 0.0632352941176471
-"122.1" "180301_13.dx" "OpenLab 1" "2018-03-01 18:38:03+01:00" 1 "P1-B-7" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Cysteine" 5.979 -0.016 0.148 -0.604 -0.604 "Norvaline" 7 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 1 1 "NA" 66.3 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -30.2 -151 -75.5 -906 -13.6651583710407 -0.0136651583710407
-"122.1" "180301_13.dx" "OpenLab 1" "2018-03-01 18:38:03+01:00" 1 "P1-B-7" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Lysine" 6.074 0.303 5.013 1.092 1.092 "Norvaline" 7 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 1 1 "NA" 66.3 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 54.6 273 136.5 1638 24.7058823529412 0.0247058823529412
-"122.1" "180301_13.dx" "OpenLab 1" "2018-03-01 18:38:03+01:00" 1 "P1-B-7" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Tyrosine" 6.264 0.716 7.511 0.692 0.692 "Norvaline" 7 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 1 1 "NA" 66.3 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 34.6 173 86.5 1038 15.6561085972851 0.0156561085972851
-"122.1" "180301_13.dx" "OpenLab 1" "2018-03-01 18:38:03+01:00" 1 "P1-B-7" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Valine" 6.7 1.156 9.593 0.548 0.548 "Norvaline" 7 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 1 1 "NA" 66.3 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 27.4 137 68.5 822 12.3981900452489 0.0123981900452489
-"122.1" "180301_13.dx" "OpenLab 1" "2018-03-01 18:38:03+01:00" 1 "P1-B-7" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Isoleucine" 7.726 -0.882 4.052 -0.303 -0.303 "Norvaline" 7 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 1 1 "NA" 66.3 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -15.15 -75.75 -37.875 -454.5 -6.8552036199095 -0.0068552036199095
-"122.1" "180301_13.dx" "OpenLab 1" "2018-03-01 18:38:03+01:00" 1 "P1-B-7" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Leucine" 7.823 -0.537 3.963 -0.487 -0.487 "Norvaline" 7 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 1 1 "NA" 66.3 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -24.35 -121.75 -60.875 -730.5 -11.0180995475113 -0.0110180995475113
-"122.1" "180301_13.dx" "OpenLab 1" "2018-03-01 18:38:03+01:00" 1 "P1-B-7" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Phenylalanine" 7.911 -0.466 4.906 -0.695 -0.695 "Norvaline" 7 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 1 1 "NA" 66.3 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -34.75 -173.75 -86.875 -1042.5 -15.7239819004525 -0.0157239819004525
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Histidine" 1.419 0.103 0.993 0.669 0.669 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 33.45 167.25 83.625 1003.5 17.855871886121 0.017855871886121
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Serine" 2.011 0.512 12.407 1.688 1.688 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 84.4 422 211 2532 45.0533807829181 0.0450533807829181
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Arginine + Glutamine" 2.068 0.248 30.235 8.497 8.497 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 424.85 2124.25 1062.125 12745.5 226.788256227758 0.226788256227758
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glycine" 2.239 -0.534 2.024 -0.264 -0.264 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -13.2 -66 -33 -396 -7.04626334519573 -0.00704626334519573
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Aspartate" 2.391 0.223 47.476 14.839 14.839 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 741.95 3709.75 1854.875 22258.5 396.05871886121 0.39605871886121
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glutamate" 2.775 0.219 61.275 19.446 19.446 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 972.3 4861.5 2430.75 29169 519.021352313167 0.519021352313167
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Threonine" 3.171 -0.019 0.361 -1.346 -1.346 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -67.3 -336.5 -168.25 -2019 -35.9252669039146 -0.0359252669039146
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Alanine" 3.62 -0.02 0.338 -1.162 -1.162 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -58.1 -290.5 -145.25 -1743 -31.0142348754448 -0.0310142348754448
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Proline" 4.322 0.28 9.384 2.329 2.329 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 116.45 582.25 291.125 3493.5 62.161921708185 0.062161921708185
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Cysteine" 5.981 -0.031 0.248 -0.563 -0.563 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -28.15 -140.75 -70.375 -844.5 -15.0266903914591 -0.0150266903914591
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Lysine" 6.075 0.338 3.73 0.769 0.769 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 38.45 192.25 96.125 1153.5 20.5249110320285 0.0205249110320285
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Tyrosine" 6.262 1.658 4.732 0.199 0.199 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 9.95 49.75 24.875 298.5 5.31138790035587 0.00531138790035587
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Valine" 6.7 -0.566 5.268 -0.648 -0.648 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -32.4 -162 -81 -972 -17.2953736654804 -0.0172953736654804
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Isoleucine" 7.728 -0.261 2.63 -0.7 -0.7 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -35 -175 -87.5 -1050 -18.6832740213523 -0.0186832740213523
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Leucine" 7.824 -0.205 2.592 -0.881 -0.881 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -44.05 -220.25 -110.125 -1321.5 -23.5142348754448 -0.0235142348754448
-"122.2" "180301_14.dx" "OpenLab 1" "2018-03-01 18:47:57+01:00" 1 "P1-B-8" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Phenylalanine" 7.912 -0.21 3.361 -1.113 -1.113 "Norvaline" 8 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 2 1 "NA" 56.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -55.65 -278.25 -139.125 -1669.5 -29.7064056939502 -0.0297064056939502
-"122.3" "180301_15.dx" "OpenLab 1" "2018-03-01 18:57:51+01:00" 1 "P1-B-9" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Histidine" 1.451 0.103 1.36 0.804 0.804 "Norvaline" 9 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 3 1 "NA" 59.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 40.2 201 100.5 1206 20.3716216216216 0.0203716216216216
-"122.3" "180301_15.dx" "OpenLab 1" "2018-03-01 18:57:51+01:00" 1 "P1-B-9" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Serine" 2.031 0.504 14.279 1.73 1.73 "Norvaline" 9 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 3 1 "NA" 59.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 86.5 432.5 216.25 2595 43.8344594594595 0.0438344594594595
-"122.3" "180301_15.dx" "OpenLab 1" "2018-03-01 18:57:51+01:00" 1 "P1-B-9" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Arginine + Glutamine" 2.097 0.248 34.189 8.419 8.419 "Norvaline" 9 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 3 1 "NA" 59.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 420.95 2104.75 1052.375 12628.5 213.319256756757 0.213319256756757
-"122.3" "180301_15.dx" "OpenLab 1" "2018-03-01 18:57:51+01:00" 1 "P1-B-9" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glycine" 2.256 -4.388 3.047 -0.042 -0.042 "Norvaline" 9 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 3 1 "NA" 59.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -2.1 -10.5 -5.25 -63 -1.06418918918919 -0.00106418918918919
-"122.3" "180301_15.dx" "OpenLab 1" "2018-03-01 18:57:51+01:00" 1 "P1-B-9" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glutamate" 2.787 0.219 70.664 19.7 19.7 "Norvaline" 9 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 3 1 "NA" 59.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 985 4925 2462.5 29550 499.155405405405 0.499155405405405
-"122.3" "180301_15.dx" "OpenLab 1" "2018-03-01 18:57:51+01:00" 1 "P1-B-9" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Threonine" 3.179 -0.013 0.295 -1.379 -1.379 "Norvaline" 9 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 3 1 "NA" 59.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -68.95 -344.75 -172.375 -2068.5 -34.9408783783784 -0.0349408783783784
-"122.3" "180301_15.dx" "OpenLab 1" "2018-03-01 18:57:51+01:00" 1 "P1-B-9" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Alanine" 3.627 -0.035 0.629 -1.092 -1.092 "Norvaline" 9 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 3 1 "NA" 59.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -54.6 -273 -136.5 -1638 -27.6689189189189 -0.0276689189189189
-"122.3" "180301_15.dx" "OpenLab 1" "2018-03-01 18:57:51+01:00" 1 "P1-B-9" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Proline" 4.327 0.28 10.764 2.351 2.351 "Norvaline" 9 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 3 1 "NA" 59.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 117.55 587.75 293.875 3526.5 59.5692567567568 0.0595692567567567
-"122.3" "180301_15.dx" "OpenLab 1" "2018-03-01 18:57:51+01:00" 1 "P1-B-9" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Cysteine" 5.982 -0.031 0.284 -0.562 -0.562 "Norvaline" 9 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 3 1 "NA" 59.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -28.1 -140.5 -70.25 -843 -14.2398648648649 -0.0142398648648649
-"122.3" "180301_15.dx" "OpenLab 1" "2018-03-01 18:57:51+01:00" 1 "P1-B-9" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Lysine" 6.076 0.345 4.09 0.724 0.724 "Norvaline" 9 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 3 1 "NA" 59.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 36.2 181 90.5 1086 18.3445945945946 0.0183445945945946
-"122.3" "180301_15.dx" "OpenLab 1" "2018-03-01 18:57:51+01:00" 1 "P1-B-9" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Tyrosine" 6.264 1.016 6.427 0.386 0.386 "Norvaline" 9 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 3 1 "NA" 59.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" 19.3 96.5 48.25 579 9.78040540540541 0.00978040540540541
-"122.3" "180301_15.dx" "OpenLab 1" "2018-03-01 18:57:51+01:00" 1 "P1-B-9" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Valine" 6.701 -0.568 6.009 -0.646 -0.646 "Norvaline" 9 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 3 1 "NA" 59.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -32.3 -161.5 -80.75 -969 -16.3682432432432 -0.0163682432432432
-"122.3" "180301_15.dx" "OpenLab 1" "2018-03-01 18:57:51+01:00" 1 "P1-B-9" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Isoleucine" 7.726 -0.303 3.191 -0.644 -0.644 "Norvaline" 9 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 3 1 "NA" 59.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -32.2 -161 -80.5 -966 -16.3175675675676 -0.0163175675675676
-"122.3" "180301_15.dx" "OpenLab 1" "2018-03-01 18:57:51+01:00" 1 "P1-B-9" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Leucine" 7.822 -0.174 2.715 -0.952 -0.952 "Norvaline" 9 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 3 1 "NA" 59.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -47.6 -238 -119 -1428 -24.1216216216216 -0.0241216216216216
-"122.3" "180301_15.dx" "OpenLab 1" "2018-03-01 18:57:51+01:00" 1 "P1-B-9" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Phenylalanine" 7.909 -0.173 3.452 -1.22 -1.22 "Norvaline" 9 "Talinum triangulare" "Leaf" "CAM" "EN" "NA" 3 1 "NA" 59.2 "80% ethanol" 1200 100 50 10 50 "CAM
-EN" -61 -305 -152.5 -1830 -30.9121621621622 -0.0309121621621622
-"19.1" "180301_07.dx" "OpenLab 1" "2018-03-01 17:38:38+01:00" 1 "P1-B-1" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Serine" 2.011 0.255 44.969 10.022 10.022 "Norvaline" 1 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 1 1 "NA" 60.7 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 501.1 2505.5 1252.75 15033 247.660626029654 0.247660626029654
-"19.1" "180301_07.dx" "OpenLab 1" "2018-03-01 17:38:38+01:00" 1 "P1-B-1" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Arginine + Glutamine" 2.074 0.217 143.799 37.692 37.692 "Norvaline" 1 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 1 1 "NA" 60.7 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 1884.6 9423 4711.5 56538 931.433278418451 0.931433278418451
-"19.1" "180301_07.dx" "OpenLab 1" "2018-03-01 17:38:38+01:00" 1 "P1-B-1" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glycine" 2.241 0.254 17.543 3.923 3.923 "Norvaline" 1 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 1 1 "NA" 60.7 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 196.15 980.75 490.375 5884.5 96.9439868204283 0.0969439868204283
-"19.1" "180301_07.dx" "OpenLab 1" "2018-03-01 17:38:38+01:00" 1 "P1-B-1" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Aspartate" 2.391 0.2 246.121 69.775 69.775 "Norvaline" 1 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 1 1 "NA" 60.7 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 3488.75 17443.75 8721.875 104662.5 1724.2586490939 1.7242586490939
-"19.1" "180301_07.dx" "OpenLab 1" "2018-03-01 17:38:38+01:00" 1 "P1-B-1" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glutamate" 2.775 0.205 280.645 77.577 77.577 "Norvaline" 1 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 1 1 "NA" 60.7 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 3878.85 19394.25 9697.125 116365.5 1917.05930807249 1.91705930807249
-"19.1" "180301_07.dx" "OpenLab 1" "2018-03-01 17:38:38+01:00" 1 "P1-B-1" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Threonine" 3.181 0.705 7.972 0.642 0.642 "Norvaline" 1 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 1 1 "NA" 60.7 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 32.1 160.5 80.25 963 15.8649093904448 0.0158649093904448
-"19.1" "180301_07.dx" "OpenLab 1" "2018-03-01 17:38:38+01:00" 1 "P1-B-1" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Alanine" 3.596 0.23 71.743 17.753 17.753 "Norvaline" 1 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 1 1 "NA" 60.7 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 887.65 4438.25 2219.125 26629.5 438.706754530478 0.438706754530478
-"19.1" "180301_07.dx" "OpenLab 1" "2018-03-01 17:38:38+01:00" 1 "P1-B-1" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Proline" 4.323 0.238 19.826 4.724 4.724 "Norvaline" 1 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 1 1 "NA" 60.7 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 236.2 1181 590.5 7086 116.73805601318 0.11673805601318
-"19.1" "180301_07.dx" "OpenLab 1" "2018-03-01 17:38:38+01:00" 1 "P1-B-1" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Lysine" 6.078 0.309 5.516 1.013 1.013 "Norvaline" 1 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 1 1 "NA" 60.7 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 50.65 253.25 126.625 1519.5 25.0329489291598 0.0250329489291598
-"19.1" "180301_07.dx" "OpenLab 1" "2018-03-01 17:38:38+01:00" 1 "P1-B-1" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Tyrosine" 6.267 -0.388 2.474 -0.362 -0.362 "Norvaline" 1 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 1 1 "NA" 60.7 "80% ethanol" 1200 100 50 10 50 "C3
-ED" -18.1 -90.5 -45.25 -543 -8.94563426688632 -0.00894563426688632
-"19.1" "180301_07.dx" "OpenLab 1" "2018-03-01 17:38:38+01:00" 1 "P1-B-1" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Methionine" 6.393 -0.019 0.856 -2.576 -2.576 "Norvaline" 1 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 1 1 "NA" 60.7 "80% ethanol" 1200 100 50 10 50 "C3
-ED" -128.8 -644 -322 -3864 -63.6573311367381 -0.0636573311367381
-"19.1" "180301_07.dx" "OpenLab 1" "2018-03-01 17:38:38+01:00" 1 "P1-B-1" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Valine" 6.703 0.33 27.794 4.789 4.789 "Norvaline" 1 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 1 1 "NA" 60.7 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 239.45 1197.25 598.625 7183.5 118.34431630972 0.11834431630972
-"19.1" "180301_07.dx" "OpenLab 1" "2018-03-01 17:38:38+01:00" 1 "P1-B-1" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Isoleucine" 7.729 0.371 13.678 2.094 2.094 "Norvaline" 1 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 1 1 "NA" 60.7 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 104.7 523.5 261.75 3141 51.7462932454695 0.0517462932454695
-"19.1" "180301_07.dx" "OpenLab 1" "2018-03-01 17:38:38+01:00" 1 "P1-B-1" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Leucine" 7.825 -0.097 2.045 -1.193 -1.193 "Norvaline" 1 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 1 1 "NA" 60.7 "80% ethanol" 1200 100 50 10 50 "C3
-ED" -59.65 -298.25 -149.125 -1789.5 -29.4810543657331 -0.0294810543657331
-"19.1" "180301_07.dx" "OpenLab 1" "2018-03-01 17:38:38+01:00" 1 "P1-B-1" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Phenylalanine" 7.912 -0.119 2.966 -1.417 -1.417 "Norvaline" 1 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 1 1 "NA" 60.7 "80% ethanol" 1200 100 50 10 50 "C3
-ED" -70.85 -354.25 -177.125 -2125.5 -35.0164744645799 -0.0350164744645799
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Histidine" 1.421 0.103 0.161 0.093 0.093 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 4.65 23.25 11.625 139.5 3.66141732283465 0.00366141732283465
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Serine" 2.021 0.299 27.148 5.421 5.421 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 271.05 1355.25 677.625 8131.5 213.425196850394 0.213425196850394
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Arginine + Glutamine" 2.086 0.221 95.22 25.738 25.738 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 1286.9 6434.5 3217.25 38607 1013.30708661417 1.01330708661417
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glycine" 2.25 0.326 8.725 1.596 1.596 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 79.8 399 199.5 2394 62.8346456692913 0.0628346456692914
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Aspartate" 2.4 0.204 150.103 43.952 43.952 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 2197.6 10988 5494 65928 1730.3937007874 1.7303937007874
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glutamate" 2.783 0.208 174.053 49.95 49.95 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 2497.5 12487.5 6243.75 74925 1966.53543307087 1.96653543307087
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Threonine" 3.187 -2.525 4.857 -0.115 -0.115 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" -5.75 -28.75 -14.375 -172.5 -4.52755905511811 -0.00452755905511811
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Alanine" 3.601 0.246 35.237 8.55 8.55 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 427.5 2137.5 1068.75 12825 336.614173228346 0.336614173228346
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Proline" 4.327 0.283 10.725 2.264 2.264 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 113.2 566 283 3396 89.1338582677165 0.0891338582677165
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Lysine" 6.078 0.534 2.58 0.288 0.288 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 14.4 72 36 432 11.3385826771654 0.0113385826771654
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Tyrosine" 6.264 -0.115 1.117 -0.581 -0.581 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" -29.05 -145.25 -72.625 -871.5 -22.8740157480315 -0.0228740157480315
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Methionine" 6.392 -0.006 0.295 -2.719 -2.719 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" -135.95 -679.75 -339.875 -4078.5 -107.047244094488 -0.107047244094488
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Valine" 6.702 0.695 12.599 1.082 1.082 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 54.1 270.5 135.25 1623 42.5984251968504 0.0425984251968504
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Isoleucine" 7.728 0.715 7.909 0.66 0.66 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 33 165 82.5 990 25.9842519685039 0.0259842519685039
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Leucine" 7.824 -0.056 1.304 -1.379 -1.379 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" -68.95 -344.75 -172.375 -2068.5 -54.2913385826772 -0.0542913385826772
-"19.2" "180301_08.dx" "OpenLab 1" "2018-03-01 17:48:33+01:00" 1 "P1-B-2" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Phenylalanine" 7.913 -0.054 1.593 -1.758 -1.758 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" -87.9 -439.5 -219.75 -2637 -69.2125984251968 -0.0692125984251969
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Histidine" 1.43 0.103 0.658 0.381 0.381 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 19.05 95.25 47.625 571.5 15 0.015
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Serine" 2.03 0.416 16.979 2.443 2.443 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 122.15 610.75 305.375 3664.5 96.1811023622047 0.0961811023622047
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Arginine + Glutamine" 2.097 0.224 78.25 20.927 20.927 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 1046.35 5231.75 2615.875 31390.5 823.897637795276 0.823897637795275
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glycine" 2.259 0.303 9.958 1.965 1.965 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 98.25 491.25 245.625 2947.5 77.3622047244095 0.0773622047244095
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Aspartate" 2.406 0.202 195.325 58.029 58.029 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 2901.45 14507.25 7253.625 87043.5 2284.6062992126 2.2846062992126
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Glutamate" 2.786 0.207 209.058 60.544 60.544 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 3027.2 15136 7568 90816 2383.62204724409 2.38362204724409
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Threonine" 3.191 0.958 6.776 0.424 0.424 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 21.2 106 53 636 16.6929133858268 0.0166929133858268
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Alanine" 3.603 0.236 49.093 12.454 12.454 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 622.7 3113.5 1556.75 18681 490.314960629921 0.490314960629921
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Proline" 4.326 0.246 16.473 4.017 4.017 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 200.85 1004.25 502.125 6025.5 158.149606299213 0.158149606299213
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Lysine" 6.078 0.343 4.216 0.736 0.736 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 36.8 184 92 1104 28.9763779527559 0.0289763779527559
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Tyrosine" 6.265 -0.409 2.402 -0.352 -0.352 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" -17.6 -88 -44 -528 -13.8582677165354 -0.0138582677165354
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Methionine" 6.391 -0.009 0.394 -2.691 -2.691 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" -134.55 -672.75 -336.375 -4036.5 -105.944881889764 -0.105944881889764
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Valine" 6.701 0.355 22.934 3.868 3.868 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 193.4 967 483.5 5802 152.283464566929 0.152283464566929
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Isoleucine" 7.726 0.416 11.339 1.633 1.633 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" 81.65 408.25 204.125 2449.5 64.2913385826772 0.0642913385826772
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Leucine" 7.822 -0.117 2.186 -1.121 -1.121 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" -56.05 -280.25 -140.125 -1681.5 -44.1338582677165 -0.0441338582677165
-"19.2" "180301_09.dx" "OpenLab 1" "2018-03-01 17:58:28+01:00" 1 "P1-B-3" "171214_ACCQ.amx" "Sample" "*2018-04-10_Amino_Acids_ISTD_NorVal.pmx" "Manual Integration" "DAD1F,Sig=260.0,16.0 Ref=324.0,8.0" "Phenylalanine" 7.91 -0.109 2.662 -1.459 -1.459 "Norvaline" 2 "Talinum triangulare" "Leaf" "C3" "ED" "NA" 2 1 "NA" 38.1 "80% ethanol" 1200 100 50 10 50 "C3
-ED" -72.95 -364.75 -182.375 -2188.5 -57.4409448818898 -0.0574409448818898
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