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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/cop_L_WT_D/cop_L_vs._WT_D_intersection_four_methods_9089.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/cop_L_WT_D/cop_L_vs._WT_D_intersection_four_methods_9089.tsv.filter_-1_1.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/cop_L_WT_D/cop_L_vs._WT_D_intersection_three_methods_9360.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/cop_L_WT_D/cop_L_vs._WT_D_intersection_three_methods_9360.tsv.filter_-1_1.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/cop_L_WT_D/edgeR/cop_L vs. WT_D_14938_edgeR_fdr.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/cop_L_WT_L/DEGpipe_cop_L vs. WT_L.log 0 → 100755
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[1] "set parameters:"
[1] "Counts file:/mnt/NAS_coruscant_datashare/haasf/madland_RNA-seq_Hoecker/31315.p.sort.counts"
[1] "Results stored at:/mnt/NAS_coruscant_datashare/haasf/madland_RNA-seq_Hoecker/DEGs_0.9"
[1] "SampleNames: cop_L" "SampleNames: WT_L"
[1] "LenGCTable: /mnt/NAS_coruscant_datashare/haasf/GeneAtlas_RNASeq/DEG_2nd_round/cosmoss_V3.3.release_2016-07-22.IsoformV31.fasta.length_GC_Contig_Daten_for_34840_1nd.csv"
[1] "myLenPos: 1"
[1] "myGCPos: 2"
[1] "rpkm: 0"
[1] "htseq: 0"
[1] "pvtedgeR: 0.001"
[1] "pvtDESeq2: 0.001"
[1] "pvtNOISeq: 0.9"
[1] "edgeRDir: edgeR"
[1] "DESeq2Dir: DESeq2"
[1] "NOISeqDir: NOISeq"
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] NOISeq_2.34.0 Matrix_1.3-3 vsn_3.58.0 gplots_3.1.1
[5] edgeR_3.32.1 limma_3.46.0 pals_1.7 gridExtra_2.3
[9] sjmisc_2.8.7 magick_2.7.2 pheatmap_1.0.12 RColorBrewer_1.1-2
[13] ggplot2_3.3.3 DESeq2_1.30.1 SummarizedExperiment_1.20.0 Biobase_2.50.0
[17] MatrixGenerics_1.2.1 matrixStats_0.58.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.7
[21] IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.36.1
loaded via a namespace (and not attached):
[1] httr_1.4.2 maps_3.3.0 bit64_4.0.5 jsonlite_1.7.2 gtools_3.8.2
[6] BiocManager_1.30.15 affy_1.68.0 blob_1.2.1 GenomeInfoDbData_1.2.4 pillar_1.6.1
[11] RSQLite_2.2.7 lattice_0.20-44 glue_1.4.2 digest_0.6.27 XVector_0.30.0
[16] colorspace_2.0-1 preprocessCore_1.52.1 htmltools_0.5.1.1 XML_3.99-0.6 pkgconfig_2.0.3
[21] genefilter_1.72.1 zlibbioc_1.36.0 purrr_0.3.4 xtable_1.8-4 scales_1.1.1
[26] affyio_1.60.0 BiocParallel_1.24.1 tibble_3.1.2 annotate_1.68.0 generics_0.1.0
[31] farver_2.1.0 sjlabelled_1.1.8 ellipsis_0.3.2 withr_2.4.2 survival_3.2-11
[36] magrittr_2.0.1 crayon_1.4.1 memoise_2.0.0 tools_4.0.5 lifecycle_1.0.0
[41] munsell_0.5.0 locfit_1.5-9.4 DelayedArray_0.16.3 AnnotationDbi_1.52.0 compiler_4.0.5
[46] caTools_1.18.2 rlang_0.4.11 grid_4.0.5 RCurl_1.98-1.3 dichromat_2.0-0
[51] rstudioapi_0.13 htmlwidgets_1.5.3 crosstalk_1.1.1 bitops_1.0-7 labeling_0.4.2
[56] gtable_0.3.0 DBI_1.1.1 R6_2.5.0 knitr_1.33 dplyr_1.0.6
[61] bit_4.0.4 insight_0.14.0 KernSmooth_2.23-20 Rcpp_1.0.6 vctrs_0.3.8
[66] mapproj_1.2.7 geneplotter_1.68.0 tidyselect_1.1.1 xfun_0.23
sysname release
"Linux" "5.4.0-72-generic"
version nodename
"#80-Ubuntu SMP Mon Apr 12 17:35:00 UTC 2021" "Ben"
machine login
"x86_64" "haasf"
user effective_user
"haasf" "haasf"
[1] "cop_L" "cop_L.1" "cop_L.2" "WT_L" "WT_L.1" "WT_L.2"
cop_L cop_L.1 cop_L.2 WT_L WT_L.1 WT_L.2
Pp3c1_20V3.1 389 389 378 299 421 446
Pp3c1_40V3.1 257 243 207 210 341 331
Pp3c1_60V3.1 475 525 521 339 533 550
Pp3c1_70V3.1 378 389 382 307 441 445
Pp3c1_80V3.1 2 3 0 0 0 0
Pp3c1_100V3.1 556 527 565 695 981 980
[1] "Raw data row number: 31315"
[1] "Raw data column number: 6"
[1] "Filtered data row number: 19456"
[1] "Filtered data row number: 6"
[1] "edgeR is running with cop_L vs. WT_L"
[1] "DESeq2 is running with cop_L vs. WT_L"
[1] "NOISeq is running with cop_L vs. WT_L"
Filtering out low count features...
18516 features are to be kept for differential expression analysis with filtering method 1
[1] "GC content bias detection is to be computed for:"
[1] "cop_L" "cop_L.1" "cop_L.2" "WT_L" "WT_L.1" "WT_L.2"
[1] "cop_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-102.377 -29.879 -0.143 24.332 180.584
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 273.01 52.29 5.221 1.32e-06 ***
bx1 -197.52 73.94 -2.671 0.00912 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 5308.39 13404.59 0.396 0.69312
bx5 -340.34 332.10 -1.025 0.30846
bx6 -64.20 80.53 -0.797 0.42765
bx7 170.19 60.32 2.821 0.00600 **
bx8 283.10 60.88 4.650 1.25e-05 ***
bx9 368.34 76.60 4.808 6.81e-06 ***
bx10 372.97 233.16 1.600 0.11352
bx11 -2522.96 1296.00 -1.947 0.05499 .
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 52.29 on 82 degrees of freedom
Multiple R-squared: 0.8304, Adjusted R-squared: 0.8118
F-statistic: 44.61 on 9 and 82 DF, p-value: < 2.2e-16
[1] "cop_L.1"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-106.832 -30.061 -0.161 23.042 186.283
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 309.02 54.50 5.670 2.08e-07 ***
bx1 -231.64 77.08 -3.005 0.00352 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 5989.38 13972.77 0.429 0.66930
bx5 -396.56 346.18 -1.146 0.25531
bx6 -89.91 83.94 -1.071 0.28726
bx7 139.69 62.88 2.222 0.02907 *
bx8 261.50 63.46 4.121 8.97e-05 ***
bx9 367.81 79.85 4.606 1.48e-05 ***
bx10 428.26 243.04 1.762 0.08178 .
bx11 -2680.24 1350.93 -1.984 0.05060 .
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 54.5 on 82 degrees of freedom
Multiple R-squared: 0.8322, Adjusted R-squared: 0.8138
F-statistic: 45.2 on 9 and 82 DF, p-value: < 2.2e-16
[1] "cop_L.2"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-107.021 -31.378 -1.905 25.842 181.678
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 309.48 53.34 5.802 1.19e-07 ***
bx1 -233.81 75.43 -3.100 0.002654 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 5700.03 13673.68 0.417 0.677869
bx5 -399.20 338.77 -1.178 0.242052
bx6 -98.01 82.15 -1.193 0.236242
bx7 140.31 61.53 2.280 0.025184 *
bx8 249.33 62.10 4.015 0.000131 ***
bx9 357.14 78.14 4.570 1.70e-05 ***
bx10 412.86 237.84 1.736 0.086343 .
bx11 -2525.66 1322.02 -1.910 0.059570 .
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 53.34 on 82 degrees of freedom
Multiple R-squared: 0.8329, Adjusted R-squared: 0.8146
F-statistic: 45.43 on 9 and 82 DF, p-value: < 2.2e-16
[1] "WT_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-87.473 -23.389 -1.215 18.713 123.849
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 270.02 41.65 6.484 6.31e-09 ***
bx1 -193.88 58.90 -3.292 0.001470 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 1208.30 10676.74 0.113 0.910172
bx5 -226.07 264.52 -0.855 0.395245
bx6 -99.47 64.14 -1.551 0.124807
bx7 89.12 48.05 1.855 0.067211 .
bx8 163.18 48.49 3.365 0.001165 **
bx9 222.87 61.01 3.653 0.000456 ***
bx10 312.73 185.71 1.684 0.095987 .
bx11 -2123.26 1032.26 -2.057 0.042875 *
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 41.65 on 82 degrees of freedom
Multiple R-squared: 0.8045, Adjusted R-squared: 0.7831
F-statistic: 37.5 on 9 and 82 DF, p-value: < 2.2e-16
[1] "WT_L.1"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-116.105 -31.078 -3.873 25.150 175.390
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 339.06 56.26 6.027 4.57e-08 ***
bx1 -234.42 79.56 -2.946 0.004184 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 2207.27 14422.60 0.153 0.878741
bx5 -301.38 357.32 -0.843 0.401428
bx6 -109.80 86.64 -1.267 0.208656
bx7 165.26 64.90 2.546 0.012757 *
bx8 264.48 65.50 4.038 0.000121 ***
bx9 355.97 82.42 4.319 4.36e-05 ***
bx10 355.15 250.87 1.416 0.160646
bx11 -2603.76 1394.43 -1.867 0.065438 .
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 56.26 on 82 degrees of freedom
Multiple R-squared: 0.8186, Adjusted R-squared: 0.7987
F-statistic: 41.11 on 9 and 82 DF, p-value: < 2.2e-16
[1] "WT_L.2"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-123.26 -34.07 -1.92 28.37 186.02
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 342.95 59.85 5.730 1.61e-07 ***
bx1 -237.63 84.64 -2.807 0.00624 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 4116.22 15344.12 0.268 0.78917
bx5 -350.86 380.15 -0.923 0.35874
bx6 -87.29 92.18 -0.947 0.34644
bx7 181.60 69.05 2.630 0.01019 *
bx8 293.16 69.68 4.207 6.57e-05 ***
bx9 383.70 87.69 4.376 3.53e-05 ***
bx10 437.46 266.89 1.639 0.10503
bx11 -2912.10 1483.52 -1.963 0.05304 .
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 59.85 on 82 degrees of freedom
Multiple R-squared: 0.8144, Adjusted R-squared: 0.794
F-statistic: 39.97 on 9 and 82 DF, p-value: < 2.2e-16
[1] "GC content bias detection is to be computed for:"
[1] "cop_L" "WT_L"
[1] "cop_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-10.5177 -3.0040 -0.0152 2.5045 18.1932
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 29.698 5.311 5.592 2.87e-07 ***
bx1 -22.115 7.510 -2.945 0.00421 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 563.957 1361.470 0.414 0.67979
bx5 -37.817 33.731 -1.121 0.26549
bx6 -8.480 8.179 -1.037 0.30287
bx7 14.841 6.127 2.422 0.01762 *
bx8 26.249 6.183 4.245 5.72e-05 ***
bx9 36.204 7.780 4.653 1.24e-05 ***
bx10 40.214 23.681 1.698 0.09328 .
bx11 -256.815 131.631 -1.951 0.05447 .
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 5.311 on 82 degrees of freedom
Multiple R-squared: 0.832, Adjusted R-squared: 0.8136
F-statistic: 45.12 on 9 and 82 DF, p-value: < 2.2e-16
[1] "WT_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-10.7519 -2.7389 -0.2344 2.3654 15.8628
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 31.654 5.192 6.097 3.38e-08 ***
bx1 -22.207 7.342 -3.025 0.003323 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 234.418 1330.946 0.176 0.860627
bx5 -28.816 32.974 -0.874 0.384731
bx6 -10.078 7.996 -1.260 0.211109
bx7 14.066 5.989 2.348 0.021258 *
bx8 23.446 6.044 3.879 0.000211 ***
bx9 31.424 7.606 4.131 8.64e-05 ***
bx10 36.477 23.150 1.576 0.118955
bx11 -252.462 128.680 -1.962 0.053163 .
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 5.192 on 82 degrees of freedom
Multiple R-squared: 0.8134, Adjusted R-squared: 0.7929
F-statistic: 39.71 on 9 and 82 DF, p-value: < 2.2e-16
[1] "cop_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-10.5177 -3.0040 -0.0152 2.5045 18.1932
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 29.698 5.311 5.592 2.87e-07 ***
bx1 -22.115 7.510 -2.945 0.00421 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 563.957 1361.470 0.414 0.67979
bx5 -37.817 33.731 -1.121 0.26549
bx6 -8.480 8.179 -1.037 0.30287
bx7 14.841 6.127 2.422 0.01762 *
bx8 26.249 6.183 4.245 5.72e-05 ***
bx9 36.204 7.780 4.653 1.24e-05 ***
bx10 40.214 23.681 1.698 0.09328 .
bx11 -256.815 131.631 -1.951 0.05447 .
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 5.311 on 82 degrees of freedom
Multiple R-squared: 0.832, Adjusted R-squared: 0.8136
F-statistic: 45.12 on 9 and 82 DF, p-value: < 2.2e-16
[1] "WT_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-10.7519 -2.7389 -0.2344 2.3654 15.8628
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 31.654 5.192 6.097 3.38e-08 ***
bx1 -22.207 7.342 -3.025 0.003323 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 234.418 1330.946 0.176 0.860627
bx5 -28.816 32.974 -0.874 0.384731
bx6 -10.078 7.996 -1.260 0.211109
bx7 14.066 5.989 2.348 0.021258 *
bx8 23.446 6.044 3.879 0.000211 ***
bx9 31.424 7.606 4.131 8.64e-05 ***
bx10 36.477 23.150 1.576 0.118955
bx11 -252.462 128.680 -1.962 0.053163 .
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 5.192 on 82 degrees of freedom
Multiple R-squared: 0.8134, Adjusted R-squared: 0.7929
F-statistic: 39.71 on 9 and 82 DF, p-value: < 2.2e-16
[1] "Length bias detection information is to be computed for:"
[1] "cop_L" "cop_L.1" "cop_L.2" "WT_L" "WT_L.1" "WT_L.2"
[1] "cop_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-75.686 -37.018 -1.886 21.809 126.426
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 815.38 47.22 17.268 < 2e-16 ***
bx1 -764.73 66.17 -11.558 < 2e-16 ***
bx2 -599.65 69.79 -8.592 5.56e-13 ***
bx3 -273.19 59.66 -4.579 1.69e-05 ***
bx4 -433.99 53.66 -8.087 5.46e-12 ***
bx5 -332.39 53.68 -6.192 2.41e-08 ***
bx6 -429.91 56.80 -7.569 5.61e-11 ***
bx7 -270.13 64.81 -4.168 7.72e-05 ***
bx8 -409.97 88.03 -4.657 1.26e-05 ***
bx9 -50.61 185.95 -0.272 0.786
bx10 -2542.52 2440.44 -1.042 0.301
bx11 40459.45 39849.79 1.015 0.313
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 47.22 on 80 degrees of freedom
Multiple R-squared: 0.7292, Adjusted R-squared: 0.692
F-statistic: 19.59 on 11 and 80 DF, p-value: < 2.2e-16
[1] "cop_L.1"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-72.783 -36.310 -3.611 22.944 132.734
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 802.79 49.42 16.244 < 2e-16 ***
bx1 -750.97 69.25 -10.844 < 2e-16 ***
bx2 -581.02 73.04 -7.955 9.92e-12 ***
bx3 -215.69 62.44 -3.454 0.000885 ***
bx4 -412.71 56.17 -7.348 1.51e-10 ***
bx5 -306.27 56.19 -5.451 5.41e-07 ***
bx6 -417.14 59.44 -7.017 6.57e-10 ***
bx7 -249.89 67.83 -3.684 0.000416 ***
bx8 -410.76 92.14 -4.458 2.67e-05 ***
bx9 -24.79 194.62 -0.127 0.898981
bx10 -2694.74 2554.23 -1.055 0.294598
bx11 42813.59 41707.92 1.027 0.307745
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 49.42 on 80 degrees of freedom
Multiple R-squared: 0.6991, Adjusted R-squared: 0.6578
F-statistic: 16.9 on 11 and 80 DF, p-value: < 2.2e-16
[1] "cop_L.2"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-72.825 -36.127 -3.231 21.950 126.840
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 838.47 47.41 17.686 < 2e-16 ***
bx1 -787.60 66.43 -11.856 < 2e-16 ***
bx2 -634.64 70.07 -9.057 6.78e-14 ***
bx3 -284.99 59.90 -4.758 8.54e-06 ***
bx4 -449.45 53.88 -8.342 1.73e-12 ***
bx5 -350.28 53.90 -6.499 6.41e-09 ***
bx6 -443.99 57.02 -7.786 2.12e-11 ***
bx7 -288.91 65.07 -4.440 2.85e-05 ***
bx8 -415.57 88.39 -4.702 1.06e-05 ***
bx9 -83.63 186.70 -0.448 0.655
bx10 -2126.74 2450.26 -0.868 0.388
bx11 32976.27 40010.23 0.824 0.412
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 47.41 on 80 degrees of freedom
Multiple R-squared: 0.7416, Adjusted R-squared: 0.706
F-statistic: 20.87 on 11 and 80 DF, p-value: < 2.2e-16
[1] "WT_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-79.55 -21.80 -2.55 19.56 98.81
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 687.49 34.96 19.664 < 2e-16 ***
bx1 -638.47 48.99 -13.032 < 2e-16 ***
bx2 -496.52 51.67 -9.609 5.61e-15 ***
bx3 -257.22 44.17 -5.823 1.15e-07 ***
bx4 -388.42 39.73 -9.775 2.65e-15 ***
bx5 -304.01 39.75 -7.648 3.94e-11 ***
bx6 -380.07 42.05 -9.038 7.40e-14 ***
bx7 -245.41 47.98 -5.115 2.11e-06 ***
bx8 -353.28 65.18 -5.420 6.14e-07 ***
bx9 -25.48 137.68 -0.185 0.854
bx10 -2286.38 1806.97 -1.265 0.209
bx11 35962.24 29505.86 1.219 0.226
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 34.96 on 80 degrees of freedom
Multiple R-squared: 0.7785, Adjusted R-squared: 0.748
F-statistic: 25.56 on 11 and 80 DF, p-value: < 2.2e-16
[1] "WT_L.1"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-97.60 -27.15 -3.12 26.30 125.06
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 1004.10 45.93 21.861 < 2e-16 ***
bx1 -941.03 64.36 -14.621 < 2e-16 ***
bx2 -776.88 67.88 -11.444 < 2e-16 ***
bx3 -446.74 58.03 -7.698 3.15e-11 ***
bx4 -585.57 52.20 -11.218 < 2e-16 ***
bx5 -463.52 52.22 -8.876 1.54e-13 ***
bx6 -559.92 55.25 -10.135 5.28e-16 ***
bx7 -373.77 63.04 -5.929 7.37e-08 ***
bx8 -512.22 85.63 -5.982 5.90e-08 ***
bx9 -52.79 180.88 -0.292 0.771
bx10 -3082.01 2373.89 -1.298 0.198
bx11 47519.91 38763.12 1.226 0.224
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 45.93 on 80 degrees of freedom
Multiple R-squared: 0.8323, Adjusted R-squared: 0.8093
F-statistic: 36.1 on 11 and 80 DF, p-value: < 2.2e-16
[1] "WT_L.2"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-105.422 -28.405 -3.742 26.842 135.613
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 986.56 50.31 19.611 < 2e-16 ***
bx1 -923.01 70.49 -13.094 < 2e-16 ***
bx2 -737.05 74.35 -9.913 1.43e-15 ***
bx3 -377.02 63.56 -5.932 7.29e-08 ***
bx4 -541.17 57.17 -9.465 1.07e-14 ***
bx5 -422.25 57.20 -7.383 1.29e-10 ***
bx6 -527.48 60.51 -8.717 3.16e-13 ***
bx7 -343.35 69.04 -4.973 3.69e-06 ***
bx8 -484.44 93.79 -5.165 1.72e-06 ***
bx9 -17.43 198.11 -0.088 0.930
bx10 -3284.72 2600.01 -1.263 0.210
bx11 51490.50 42455.34 1.213 0.229
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 50.31 on 80 degrees of freedom
Multiple R-squared: 0.7896, Adjusted R-squared: 0.7607
F-statistic: 27.3 on 11 and 80 DF, p-value: < 2.2e-16
[1] "Length bias detection information is to be computed for:"
[1] "cop_L" "WT_L"
[1] "cop_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-7.2225 -3.4420 -0.2094 2.1574 12.8616
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 81.557 4.777 17.073 < 2e-16 ***
bx1 -76.467 6.694 -11.424 < 2e-16 ***
bx2 -60.294 7.060 -8.540 7.04e-13 ***
bx3 -25.693 6.035 -4.257 5.59e-05 ***
bx4 -43.035 5.429 -7.927 1.12e-11 ***
bx5 -32.855 5.431 -6.050 4.42e-08 ***
bx6 -42.843 5.746 -7.457 9.30e-11 ***
bx7 -26.878 6.556 -4.100 9.86e-05 ***
bx8 -41.025 8.906 -4.607 1.52e-05 ***
bx9 -5.335 18.812 -0.284 0.777
bx10 -243.901 246.886 -0.988 0.326
bx11 3850.493 4031.380 0.955 0.342
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 4.777 on 80 degrees of freedom
Multiple R-squared: 0.7234, Adjusted R-squared: 0.6854
F-statistic: 19.02 on 11 and 80 DF, p-value: < 2.2e-16
[1] "WT_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-9.3891 -2.5105 -0.1581 2.4499 11.9227
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 88.163 4.325 20.384 < 2e-16 ***
bx1 -82.320 6.061 -13.583 < 2e-16 ***
bx2 -65.929 6.392 -10.314 2.37e-16 ***
bx3 -35.398 5.465 -6.478 7.02e-09 ***
bx4 -49.870 4.916 -10.145 5.04e-16 ***
bx5 -39.175 4.917 -7.967 9.41e-12 ***
bx6 -48.352 5.202 -9.294 2.32e-14 ***
bx7 -31.689 5.936 -5.338 8.56e-07 ***
bx8 -44.532 8.064 -5.523 4.03e-07 ***
bx9 -3.031 17.033 -0.178 0.859
bx10 -287.684 223.541 -1.287 0.202
bx11 4494.237 3650.185 1.231 0.222
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 4.325 on 80 degrees of freedom
Multiple R-squared: 0.8012, Adjusted R-squared: 0.7738
F-statistic: 29.31 on 11 and 80 DF, p-value: < 2.2e-16
[1] "cop_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-7.2225 -3.4420 -0.2094 2.1574 12.8616
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 81.557 4.777 17.073 < 2e-16 ***
bx1 -76.467 6.694 -11.424 < 2e-16 ***
bx2 -60.294 7.060 -8.540 7.04e-13 ***
bx3 -25.693 6.035 -4.257 5.59e-05 ***
bx4 -43.035 5.429 -7.927 1.12e-11 ***
bx5 -32.855 5.431 -6.050 4.42e-08 ***
bx6 -42.843 5.746 -7.457 9.30e-11 ***
bx7 -26.878 6.556 -4.100 9.86e-05 ***
bx8 -41.025 8.906 -4.607 1.52e-05 ***
bx9 -5.335 18.812 -0.284 0.777
bx10 -243.901 246.886 -0.988 0.326
bx11 3850.493 4031.380 0.955 0.342
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 4.777 on 80 degrees of freedom
Multiple R-squared: 0.7234, Adjusted R-squared: 0.6854
F-statistic: 19.02 on 11 and 80 DF, p-value: < 2.2e-16
[1] "WT_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-9.3891 -2.5105 -0.1581 2.4499 11.9227
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 88.163 4.325 20.384 < 2e-16 ***
bx1 -82.320 6.061 -13.583 < 2e-16 ***
bx2 -65.929 6.392 -10.314 2.37e-16 ***
bx3 -35.398 5.465 -6.478 7.02e-09 ***
bx4 -49.870 4.916 -10.145 5.04e-16 ***
bx5 -39.175 4.917 -7.967 9.41e-12 ***
bx6 -48.352 5.202 -9.294 2.32e-14 ***
bx7 -31.689 5.936 -5.338 8.56e-07 ***
bx8 -44.532 8.064 -5.523 4.03e-07 ***
bx9 -3.031 17.033 -0.178 0.859
bx10 -287.684 223.541 -1.287 0.202
bx11 4494.237 3650.185 1.231 0.222
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 4.325 on 80 degrees of freedom
Multiple R-squared: 0.8012, Adjusted R-squared: 0.7738
F-statistic: 29.31 on 11 and 80 DF, p-value: < 2.2e-16
[1] "Reference sample is: cop_L"
[1] "Confidence intervals for median of M:"
0.5% 99.5% Diagnostic Test
cop_L.1 "-0.0142646625042663" "-0.00695797589426857" "FAILED"
cop_L.2 "-0.00668523582332182" "-8.14922150691232e-05" "FAILED"
WT_L "0.0202666845937637" "0.0383079441873668" "FAILED"
WT_L.1 "0.0510610061745732" "0.0689723022177598" "FAILED"
WT_L.2 "0.048196454730509" "0.0654941209576264" "FAILED"
[1] "Diagnostic test: FAILED. Normalization is required to correct this bias."
[1] "WARNING: Your experiment has biological replicates. You should consider using NOISeqBIO instead of NOISeq."
[1] "Computing (M,D) values..."
[1] "Computing probability of differential expression..."
[1] "WARNING: Your experiment has biological replicates. You should consider using NOISeqBIO instead of NOISeq."
[1] "Computing (M,D) values..."
[1] "Computing probability of differential expression..."
[1] "WARNING: Your experiment has biological replicates. You should consider using NOISeqBIO instead of NOISeq."
[1] "Computing (M,D) values..."
[1] "Computing probability of differential expression..."
Computing Z values...
Filtering out low count features...
17750 features are to be kept for differential expression analysis with filtering method 1
...k-means clustering done
Size of 15 clusters:
[1] 4693 273 503 2838 1562 63 17 27 915 166 3 103 37 339 6211
Resampling cluster...[1] 1
Size of 15 subclusters of cluster: 1
[1] 460 378 183 94 634 348 202 274 352 203 501 572 360 95 37
[1] 2
[1] 3
[1] 4
Size of 15 subclusters of cluster: 4
[1] 19 370 55 205 271 190 156 114 258 206 27 84 235 383 265
[1] 5
Size of 15 subclusters of cluster: 5
[1] 173 6 142 65 93 37 32 210 70 146 187 50 143 95 113
[1] 6
[1] 7
[1] 8
[1] 9
[1] 10
[1] 11
[1] 12
[1] 13
[1] 14
[1] 15
Size of 15 subclusters of cluster: 15
[1] 281 920 593 457 714 306 276 717 80 503 73 533 192 305 261
Computing Z for noise...
Computing probability of differential expression...
p0 = 0.192292690112028
Probability
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.7679 0.9331 0.8048 0.9740 1.0000 766
Computing Z values...
Filtering out low count features...
18516 features are to be kept for differential expression analysis with filtering method 1
...k-means clustering done
Size of 15 clusters:
[1] 169 37 4980 6578 914 2 503 61 104 2937 272 12 1575 30 342
Resampling cluster...[1] 1
[1] 2
[1] 3
Size of 15 subclusters of cluster: 3
[1] 314 750 31 91 332 504 502 588 502 234 202 103 288 173 366
[1] 4
Size of 15 subclusters of cluster: 4
[1] 44 584 619 376 853 1241 186 60 185 309 449 409 403 588 272
[1] 5
[1] 6
[1] 7
[1] 8
[1] 9
[1] 10
Size of 15 subclusters of cluster: 10
[1] 218 366 233 287 272 175 17 112 51 64 283 426 187 216 30
[1] 11
[1] 12
[1] 13
Size of 15 subclusters of cluster: 13
[1] 121 159 98 179 83 206 28 166 166 63 143 90 28 39 6
[1] 14
[1] 15
Computing Z for noise...
Computing probability of differential expression...
p0 = 0.199043087787024
Probability
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.0000 0.7454 0.9233 0.7962 0.9671 1.0000
Computing Z values...
Filtering out low count features...
18516 features are to be kept for differential expression analysis with filtering method 1
...k-means clustering done
Size of 15 clusters:
[1] 33 3141 1209 5776 52 110 187 4434 16 3 480 772 1973 16 314
Resampling cluster...[1] 1
[1] 2
Size of 15 subclusters of cluster: 2
[1] 241 241 284 82 266 232 257 10 77 200 45 412 79 354 361
[1] 3
Size of 15 subclusters of cluster: 3
[1] 32 24 72 111 16 100 136 41 149 4 136 80 102 188 18
[1] 4
Size of 15 subclusters of cluster: 4
[1] 571 102 368 339 459 259 463 739 136 247 1177 207 363 104 242
[1] 5
[1] 6
[1] 7
[1] 8
Size of 15 subclusters of cluster: 8
[1] 231 74 275 432 543 323 439 131 311 71 437 444 226 435 62
[1] 9
[1] 10
[1] 11
[1] 12
[1] 13
Size of 15 subclusters of cluster: 13
[1] 264 67 68 80 152 225 160 51 236 192 135 132 167 16 28
[1] 14
[1] 15
Computing Z for noise...
Computing probability of differential expression...
p0 = 0.355730135684947
Probability
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.0000 0.4078 0.7690 0.6398 0.8932 1.0000
[1] "1704 differentially expressed features"
[1] "913 differentially expressed features (up in first condition)"
[1] "791 differentially expressed features (down in first condition)"
[1] "405 differentially expressed features"
[1] "209 differentially expressed features (up in first condition)"
[1] "196 differentially expressed features (down in first condition)"
[1] "1810 differentially expressed features"
[1] "4064 differentially expressed features"
[1] "634 differentially expressed features"
[1] "1303 differentially expressed features"
[1] "1849 differentially expressed features"
[1] "4178 differentially expressed features"
[1] "10458 differentially expressed features"
[1] "1704 differentially expressed features"
[1] "4246 differentially expressed features"
[1] "405 differentially expressed features"
[1] "1810 differentially expressed features"
[1] "634 differentially expressed features"
[1] "DEGs edgeR"
[1] 5829
[1] "DEGs deseq2"
[1] 4265
[1] "DEGs noiseq"
[1] 1810
[1] "DEGs noiseqbio"
[1] 1704
[1] "DEGs intersection without direction check (four methods)"
[1] 1193
[1] "Pp3c1_100V3.1" "Pp3c1_470V3.1" "Pp3c1_540V3.1" "Pp3c1_690V3.1" "Pp3c1_1870V3.1" "Pp3c1_1940V3.1"
[7] "Pp3c1_2420V3.1" "Pp3c1_3200V3.1" "Pp3c1_3260V3.1" "Pp3c1_4270V3.1" "Pp3c1_4400V3.1" "Pp3c1_4750V3.1"
[13] "Pp3c1_5050V3.1" "Pp3c1_5300V3.1" "Pp3c1_5870V3.1" "Pp3c1_6640V3.1" "Pp3c1_7370V3.1" "Pp3c1_7380V3.1"
[19] "Pp3c1_7540V3.1" "Pp3c1_7910V3.1" "Pp3c1_9320V3.1" "Pp3c1_9560V3.1" "Pp3c1_10010V3.1" "Pp3c1_10180V3.1"
[25] "Pp3c1_10470V3.1" "Pp3c1_10970V3.1" "Pp3c1_11030V3.1" "Pp3c1_12470V3.1" "Pp3c1_13170V3.1" "Pp3c1_13570V3.1"
[31] "Pp3c1_13910V3.1" "Pp3c1_15150V3.1" "Pp3c1_15690V3.1" "Pp3c1_16840V3.1" "Pp3c1_17080V3.1" "Pp3c1_17220V3.1"
[37] "Pp3c1_18860V3.1" "Pp3c1_19060V3.1" "Pp3c1_20430V3.1" "Pp3c1_20700V3.1" "Pp3c1_20980V3.1" "Pp3c1_21540V3.1"
[43] "Pp3c1_21890V3.1" "Pp3c1_22450V3.1" "Pp3c1_24000V3.1" "Pp3c1_24790V3.1" "Pp3c1_25770V3.1" "Pp3c1_25980V3.1"
[49] "Pp3c1_26200V3.1" "Pp3c1_27270V3.1" "Pp3c1_27440V3.1" "Pp3c1_28390V3.1" "Pp3c1_29300V3.1" "Pp3c1_29630V3.1"
[55] "Pp3c1_29650V3.1" "Pp3c1_30150V3.1" "Pp3c1_30410V3.1" "Pp3c1_30570V3.1" "Pp3c1_30660V3.1" "Pp3c1_30790V3.1"
[61] "Pp3c1_31720V3.1" "Pp3c1_31850V3.1" "Pp3c1_32350V3.1" "Pp3c1_32810V3.1" "Pp3c1_32910V3.1" "Pp3c1_33050V3.1"
[67] "Pp3c1_33470V3.1" "Pp3c1_33480V3.1" "Pp3c1_33830V3.1" "Pp3c1_34890V3.1" "Pp3c1_35100V3.1" "Pp3c1_37110V3.1"
[73] "Pp3c1_38210V3.1" "Pp3c1_38250V3.1" "Pp3c1_38340V3.1" "Pp3c1_38440V3.1" "Pp3c1_38880V3.1" "Pp3c1_39540V3.1"
[79] "Pp3c1_39640V3.1" "Pp3c1_39780V3.1" "Pp3c1_39990V3.1" "Pp3c1_40040V3.1" "Pp3c1_40610V3.1" "Pp3c1_40790V3.1"
[85] "Pp3c2_181V3.1" "Pp3c2_200V3.1" "Pp3c2_1280V3.1" "Pp3c2_2120V3.1" "Pp3c2_2520V3.1" "Pp3c2_2730V3.1"
[91] "Pp3c2_2760V3.1" "Pp3c2_2830V3.1" "Pp3c2_3490V3.1" "Pp3c2_4100V3.1" "Pp3c2_4500V3.1" "Pp3c2_6410V3.1"
[97] "Pp3c2_6630V3.1" "Pp3c2_6690V3.1" "Pp3c2_6750V3.1" "Pp3c2_8420V3.1" "Pp3c2_8660V3.1" "Pp3c2_9460V3.1"
[103] "Pp3c2_10260V3.1" "Pp3c2_10530V3.1" "Pp3c2_12080V3.1" "Pp3c2_12150V3.1" "Pp3c2_13280V3.1" "Pp3c2_13670V3.1"
[109] "Pp3c2_14290V3.1" "Pp3c2_14400V3.1" "Pp3c2_15140V3.1" "Pp3c2_17110V3.1" "Pp3c2_17290V3.1" "Pp3c2_17450V3.1"
[115] "Pp3c2_17670V3.1" "Pp3c2_17700V3.1" "Pp3c2_20450V3.1" "Pp3c2_20840V3.1" "Pp3c2_22000V3.1" "Pp3c2_22140V3.1"
[121] "Pp3c2_24160V3.1" "Pp3c2_24620V3.1" "Pp3c2_25720V3.1" "Pp3c2_25890V3.1" "Pp3c2_28030V3.1" "Pp3c2_29140V3.1"
[127] "Pp3c2_29420V3.1" "Pp3c2_29720V3.1" "Pp3c2_30230V3.1" "Pp3c2_30630V3.1" "Pp3c2_30980V3.1" "Pp3c2_32540V3.1"
[133] "Pp3c2_32770V3.1" "Pp3c2_34310V3.1" "Pp3c2_35010V3.1" "Pp3c2_35740V3.1" "Pp3c2_35950V3.1" "Pp3c2_36790V3.1"
[139] "Pp3c2_37190V3.1" "Pp3c2_37299V3.1" "Pp3c2_37670V3.1" "Pp3c2_38120V3.1" "Pp3c3_240V3.1" "Pp3c3_330V3.1"
[145] "Pp3c3_1164V3.1" "Pp3c3_1650V3.1" "Pp3c3_2130V3.1" "Pp3c3_2760V3.1" "Pp3c3_3070V3.1" "Pp3c3_4090V3.1"
[151] "Pp3c3_4970V3.1" "Pp3c3_5810V3.1" "Pp3c3_5930V3.1" "Pp3c3_6370V3.1" "Pp3c3_7020V3.1" "Pp3c3_7180V3.1"
[157] "Pp3c3_7440V3.1" "Pp3c3_8880V3.1" "Pp3c3_9200V3.1" "Pp3c3_10140V3.1" "Pp3c3_10250V3.1" "Pp3c3_10350V3.1"
[163] "Pp3c3_10730V3.1" "Pp3c3_11230V3.1" "Pp3c3_11730V3.1" "Pp3c3_11770V3.1" "Pp3c3_11840V3.1" "Pp3c3_11932V3.1"
[169] "Pp3c3_12090V3.1" "Pp3c3_12760V3.1" "Pp3c3_13220V3.1" "Pp3c3_13550V3.1" "Pp3c3_15040V3.1" "Pp3c3_16280V3.1"
[175] "Pp3c3_16880V3.1" "Pp3c3_17340V3.1" "Pp3c3_17950V3.1" "Pp3c3_18750V3.1" "Pp3c3_19510V3.1" "Pp3c3_19580V3.1"
[181] "Pp3c3_20390V3.1" "Pp3c3_21440V3.1" "Pp3c3_22090V3.1" "Pp3c3_22490V3.1" "Pp3c3_22750V3.1" "Pp3c3_22850V3.1"
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[193] "Pp3c3_28810V3.1" "Pp3c3_29530V3.1" "Pp3c3_29970V3.1" "Pp3c3_30140V3.1" "Pp3c3_30150V3.1" "Pp3c3_30210V3.1"
[199] "Pp3c3_30710V3.1" "Pp3c3_30990V3.1" "Pp3c3_31900V3.1" "Pp3c3_32390V3.1" "Pp3c3_32490V3.1" "Pp3c3_32790V3.1"
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[277] "Pp3c5_3160V3.1" "Pp3c5_3210V3.1" "Pp3c5_3300V3.1" "Pp3c5_3400V3.1" "Pp3c5_4200V3.1" "Pp3c5_4230V3.1"
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[295] "Pp3c5_10760V3.1" "Pp3c5_10920V3.1" "Pp3c5_10960V3.1" "Pp3c5_11200V3.1" "Pp3c5_11390V3.1" "Pp3c5_12950V3.1"
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[715] "Pp3c14_19950V3.1" "Pp3c14_20300V3.1" "Pp3c14_20510V3.1" "Pp3c14_20830V3.1" "Pp3c14_21300V3.1" "Pp3c14_21530V3.1"
[721] "Pp3c14_22334V3.1" "Pp3c14_22510V3.1" "Pp3c14_22690V3.1" "Pp3c14_22910V3.1" "Pp3c14_24300V3.1" "Pp3c14_24340V3.1"
[727] "Pp3c14_26600V3.1" "Pp3c15_680V3.1" "Pp3c15_710V3.1" "Pp3c15_830V3.1" "Pp3c15_890V3.1" "Pp3c15_1320V3.1"
[733] "Pp3c15_1630V3.1" "Pp3c15_2570V3.1" "Pp3c15_2630V3.1" "Pp3c15_3930V3.1" "Pp3c15_4170V3.1" "Pp3c15_4260V3.1"
[739] "Pp3c15_4460V3.1" "Pp3c15_5850V3.1" "Pp3c15_6160V3.1" "Pp3c15_6290V3.1" "Pp3c15_7750V3.1" "Pp3c15_7930V3.1"
[745] "Pp3c15_9220V3.1" "Pp3c15_10210V3.1" "Pp3c15_10400V3.1" "Pp3c15_10680V3.1" "Pp3c15_12010V3.1" "Pp3c15_12130V3.1"
[751] "Pp3c15_12980V3.1" "Pp3c15_13040V3.1" "Pp3c15_13550V3.1" "Pp3c15_13650V3.1" "Pp3c15_14640V3.1" "Pp3c15_14890V3.1"
[757] "Pp3c15_14930V3.1" "Pp3c15_15020V3.1" "Pp3c15_15470V3.1" "Pp3c15_16510V3.1" "Pp3c15_16690V3.1" "Pp3c15_18090V3.1"
[763] "Pp3c15_18140V3.1" "Pp3c15_18270V3.1" "Pp3c15_18400V3.1" "Pp3c15_18500V3.1" "Pp3c15_19080V3.1" "Pp3c15_19160V3.1"
[769] "Pp3c15_19950V3.1" "Pp3c15_20650V3.1" "Pp3c15_22720V3.1" "Pp3c15_22730V3.1" "Pp3c15_23370V3.1" "Pp3c15_23520V3.1"
[775] "Pp3c15_23590V3.1" "Pp3c15_23960V3.1" "Pp3c15_24030V3.1" "Pp3c15_24050V3.1" "Pp3c15_25660V3.1" "Pp3c16_2540V3.1"
[781] "Pp3c16_3080V3.1" "Pp3c16_4550V3.1" "Pp3c16_4660V3.1" "Pp3c16_6440V3.1" "Pp3c16_6730V3.1" "Pp3c16_6980V3.1"
[787] "Pp3c16_7180V3.1" "Pp3c16_7660V3.1" "Pp3c16_8090V3.1" "Pp3c16_8260V3.1" "Pp3c16_8430V3.1" "Pp3c16_8500V3.1"
[793] "Pp3c16_8850V3.1" "Pp3c16_10460V3.1" "Pp3c16_11320V3.1" "Pp3c16_11630V3.1" "Pp3c16_11800V3.1" "Pp3c16_13700V3.1"
[799] "Pp3c16_14220V3.1" "Pp3c16_14400V3.1" "Pp3c16_15270V3.1" "Pp3c16_15860V3.1" "Pp3c16_16440V3.1" "Pp3c16_16680V3.1"
[805] "Pp3c16_17280V3.1" "Pp3c16_18590V3.1" "Pp3c16_18700V3.1" "Pp3c16_18710V3.1" "Pp3c16_19530V3.1" "Pp3c16_20890V3.1"
[811] "Pp3c16_21250V3.1" "Pp3c16_21900V3.1" "Pp3c16_22280V3.1" "Pp3c16_22330V3.1" "Pp3c16_22430V3.1" "Pp3c16_22550V3.1"
[817] "Pp3c16_22650V3.1" "Pp3c16_23230V3.1" "Pp3c16_24460V3.1" "Pp3c16_25600V3.1" "Pp3c16_25860V3.1" "Pp3c17_5070V3.1"
[823] "Pp3c17_5130V3.1" "Pp3c17_5320V3.1" "Pp3c17_5990V3.1" "Pp3c17_6090V3.1" "Pp3c17_7480V3.1" "Pp3c17_7560V3.1"
[829] "Pp3c17_7680V3.1" "Pp3c17_7790V3.1" "Pp3c17_9810V3.1" "Pp3c17_10170V3.1" "Pp3c17_12450V3.1" "Pp3c17_12980V3.1"
[835] "Pp3c17_13330V3.1" "Pp3c17_13940V3.1" "Pp3c17_14660V3.1" "Pp3c17_15380V3.1" "Pp3c17_15490V3.1" "Pp3c17_15920V3.1"
[841] "Pp3c17_16620V3.1" "Pp3c17_16790V3.1" "Pp3c17_17180V3.1" "Pp3c17_17840V3.1" "Pp3c17_19540V3.1" "Pp3c17_19570V3.1"
[847] "Pp3c17_20040V3.1" "Pp3c17_20310V3.1" "Pp3c17_21100V3.1" "Pp3c17_21120V3.1" "Pp3c17_21430V3.1" "Pp3c17_22200V3.1"
[853] "Pp3c17_23030V3.1" "Pp3c17_23180V3.1" "Pp3c17_23450V3.1" "Pp3c17_23740V3.1" "Pp3c17_24100V3.1" "Pp3c18_310V3.1"
[859] "Pp3c18_2170V3.1" "Pp3c18_3460V3.1" "Pp3c18_5680V3.1" "Pp3c18_5720V3.1" "Pp3c18_6179V3.1" "Pp3c18_6510V3.1"
[865] "Pp3c18_7740V3.1" "Pp3c18_7860V3.1" "Pp3c18_8240V3.1" "Pp3c18_8820V3.1" "Pp3c18_9820V3.1" "Pp3c18_9840V3.1"
[871] "Pp3c18_10760V3.1" "Pp3c18_10780V3.1" "Pp3c18_11000V3.1" "Pp3c18_13090V3.1" "Pp3c18_13570V3.1" "Pp3c18_14350V3.1"
[877] "Pp3c18_16700V3.1" "Pp3c18_18390V3.1" "Pp3c18_18460V3.1" "Pp3c18_18530V3.1" "Pp3c18_18670V3.1" "Pp3c18_19220V3.1"
[883] "Pp3c18_19690V3.1" "Pp3c18_19850V3.1" "Pp3c18_19990V3.1" "Pp3c18_20510V3.1" "Pp3c19_1490V3.1" "Pp3c19_1710V3.1"
[889] "Pp3c19_1760V3.1" "Pp3c19_2740V3.1" "Pp3c19_2860V3.1" "Pp3c19_3740V3.1" "Pp3c19_3750V3.1" "Pp3c19_4313V3.1"
[895] "Pp3c19_4500V3.1" "Pp3c19_4640V3.1" "Pp3c19_4900V3.1" "Pp3c19_5110V3.1" "Pp3c19_5510V3.1" "Pp3c19_6050V3.1"
[901] "Pp3c19_6670V3.1" "Pp3c19_6700V3.1" "Pp3c19_6710V3.1" "Pp3c19_7960V3.1" "Pp3c19_8330V3.1" "Pp3c19_8770V3.1"
[907] "Pp3c19_13170V3.1" "Pp3c19_14460V3.1" "Pp3c19_15500V3.1" "Pp3c19_15590V3.1" "Pp3c19_15790V3.1" "Pp3c19_15800V3.1"
[913] "Pp3c19_16810V3.1" "Pp3c19_17080V3.1" "Pp3c19_17290V3.1" "Pp3c19_19970V3.1" "Pp3c19_20160V3.1" "Pp3c19_20230V3.1"
[919] "Pp3c19_20270V3.1" "Pp3c19_20540V3.1" "Pp3c19_20720V3.1" "Pp3c19_20750V3.1" "Pp3c19_20780V3.1" "Pp3c19_20830V3.1"
[925] "Pp3c19_22410V3.1" "Pp3c20_1560V3.1" "Pp3c20_1800V3.1" "Pp3c20_1940V3.1" "Pp3c20_2280V3.1" "Pp3c20_2330V3.1"
[931] "Pp3c20_2890V3.1" "Pp3c20_2980V3.1" "Pp3c20_3610V3.1" "Pp3c20_3750V3.1" "Pp3c20_4670V3.1" "Pp3c20_5530V3.1"
[937] "Pp3c20_6430V3.1" "Pp3c20_7050V3.1" "Pp3c20_7850V3.1" "Pp3c20_7860V3.1" "Pp3c20_8330V3.1" "Pp3c20_9200V3.1"
[943] "Pp3c20_10210V3.1" "Pp3c20_10270V3.1" "Pp3c20_10460V3.1" "Pp3c20_10830V3.1" "Pp3c20_11000V3.1" "Pp3c20_12850V3.1"
[949] "Pp3c20_12980V3.1" "Pp3c20_14280V3.1" "Pp3c20_15780V3.1" "Pp3c20_16210V3.1" "Pp3c20_16950V3.1" "Pp3c20_17620V3.1"
[955] "Pp3c20_17800V3.1" "Pp3c20_17990V3.1" "Pp3c20_19960V3.1" "Pp3c20_21960V3.1" "Pp3c20_21990V3.1" "Pp3c20_22450V3.1"
[961] "Pp3c20_22760V3.1" "Pp3c20_22830V3.1" "Pp3c20_22890V3.1" "Pp3c20_23430V3.1" "Pp3c20_23560V3.1" "Pp3c21_180V3.1"
[967] "Pp3c21_1210V3.1" "Pp3c21_5070V3.1" "Pp3c21_5560V3.1" "Pp3c21_6150V3.1" "Pp3c21_6200V3.1" "Pp3c21_6390V3.1"
[973] "Pp3c21_6920V3.1" "Pp3c21_7810V3.1" "Pp3c21_8670V3.1" "Pp3c21_8940V3.1" "Pp3c21_9220V3.1" "Pp3c21_9380V3.1"
[979] "Pp3c21_9970V3.1" "Pp3c21_10000V3.1" "Pp3c21_10620V3.1" "Pp3c21_12100V3.1" "Pp3c21_12310V3.1" "Pp3c21_13720V3.1"
[985] "Pp3c21_14540V3.1" "Pp3c21_14830V3.1" "Pp3c21_15140V3.1" "Pp3c21_15660V3.1" "Pp3c21_16670V3.1" "Pp3c21_17930V3.1"
[991] "Pp3c21_18980V3.1" "Pp3c21_19760V3.1" "Pp3c21_21410V3.1" "Pp3c21_21800V3.1" "Pp3c22_1450V3.1" "Pp3c22_1930V3.1"
[997] "Pp3c22_3550V3.1" "Pp3c22_3910V3.1" "Pp3c22_4630V3.1" "Pp3c22_5470V3.1"
[ reached getOption("max.print") -- omitted 193 entries ]
[1] "DEGs intersection with direction check"
[1] 1193
[1] "Pp3c1_100V3.1" "Pp3c1_470V3.1" "Pp3c1_540V3.1" "Pp3c1_690V3.1" "Pp3c1_1870V3.1" "Pp3c1_1940V3.1"
[7] "Pp3c1_2420V3.1" "Pp3c1_3200V3.1" "Pp3c1_3260V3.1" "Pp3c1_4270V3.1" "Pp3c1_4400V3.1" "Pp3c1_4750V3.1"
[13] "Pp3c1_5050V3.1" "Pp3c1_5300V3.1" "Pp3c1_5870V3.1" "Pp3c1_6640V3.1" "Pp3c1_7370V3.1" "Pp3c1_7380V3.1"
[19] "Pp3c1_7540V3.1" "Pp3c1_7910V3.1" "Pp3c1_9320V3.1" "Pp3c1_9560V3.1" "Pp3c1_10010V3.1" "Pp3c1_10180V3.1"
[25] "Pp3c1_10470V3.1" "Pp3c1_10970V3.1" "Pp3c1_11030V3.1" "Pp3c1_12470V3.1" "Pp3c1_13170V3.1" "Pp3c1_13570V3.1"
[31] "Pp3c1_13910V3.1" "Pp3c1_15150V3.1" "Pp3c1_15690V3.1" "Pp3c1_16840V3.1" "Pp3c1_17080V3.1" "Pp3c1_17220V3.1"
[37] "Pp3c1_18860V3.1" "Pp3c1_19060V3.1" "Pp3c1_20430V3.1" "Pp3c1_20700V3.1" "Pp3c1_20980V3.1" "Pp3c1_21540V3.1"
[43] "Pp3c1_21890V3.1" "Pp3c1_22450V3.1" "Pp3c1_24000V3.1" "Pp3c1_24790V3.1" "Pp3c1_25770V3.1" "Pp3c1_25980V3.1"
[49] "Pp3c1_26200V3.1" "Pp3c1_27270V3.1" "Pp3c1_27440V3.1" "Pp3c1_28390V3.1" "Pp3c1_29300V3.1" "Pp3c1_29630V3.1"
[55] "Pp3c1_29650V3.1" "Pp3c1_30150V3.1" "Pp3c1_30410V3.1" "Pp3c1_30570V3.1" "Pp3c1_30660V3.1" "Pp3c1_30790V3.1"
[61] "Pp3c1_31720V3.1" "Pp3c1_31850V3.1" "Pp3c1_32350V3.1" "Pp3c1_32810V3.1" "Pp3c1_32910V3.1" "Pp3c1_33050V3.1"
[67] "Pp3c1_33470V3.1" "Pp3c1_33480V3.1" "Pp3c1_33830V3.1" "Pp3c1_34890V3.1" "Pp3c1_35100V3.1" "Pp3c1_37110V3.1"
[73] "Pp3c1_38210V3.1" "Pp3c1_38250V3.1" "Pp3c1_38340V3.1" "Pp3c1_38440V3.1" "Pp3c1_38880V3.1" "Pp3c1_39540V3.1"
[79] "Pp3c1_39640V3.1" "Pp3c1_39780V3.1" "Pp3c1_39990V3.1" "Pp3c1_40040V3.1" "Pp3c1_40610V3.1" "Pp3c1_40790V3.1"
[85] "Pp3c2_181V3.1" "Pp3c2_200V3.1" "Pp3c2_1280V3.1" "Pp3c2_2120V3.1" "Pp3c2_2520V3.1" "Pp3c2_2730V3.1"
[91] "Pp3c2_2760V3.1" "Pp3c2_2830V3.1" "Pp3c2_3490V3.1" "Pp3c2_4100V3.1" "Pp3c2_4500V3.1" "Pp3c2_6410V3.1"
[97] "Pp3c2_6630V3.1" "Pp3c2_6690V3.1" "Pp3c2_6750V3.1" "Pp3c2_8420V3.1" "Pp3c2_8660V3.1" "Pp3c2_9460V3.1"
[103] "Pp3c2_10260V3.1" "Pp3c2_10530V3.1" "Pp3c2_12080V3.1" "Pp3c2_12150V3.1" "Pp3c2_13280V3.1" "Pp3c2_13670V3.1"
[109] "Pp3c2_14290V3.1" "Pp3c2_14400V3.1" "Pp3c2_15140V3.1" "Pp3c2_17110V3.1" "Pp3c2_17290V3.1" "Pp3c2_17450V3.1"
[115] "Pp3c2_17670V3.1" "Pp3c2_17700V3.1" "Pp3c2_20450V3.1" "Pp3c2_20840V3.1" "Pp3c2_22000V3.1" "Pp3c2_22140V3.1"
[121] "Pp3c2_24160V3.1" "Pp3c2_24620V3.1" "Pp3c2_25720V3.1" "Pp3c2_25890V3.1" "Pp3c2_28030V3.1" "Pp3c2_29140V3.1"
[127] "Pp3c2_29420V3.1" "Pp3c2_29720V3.1" "Pp3c2_30230V3.1" "Pp3c2_30630V3.1" "Pp3c2_30980V3.1" "Pp3c2_32540V3.1"
[133] "Pp3c2_32770V3.1" "Pp3c2_34310V3.1" "Pp3c2_35010V3.1" "Pp3c2_35740V3.1" "Pp3c2_35950V3.1" "Pp3c2_36790V3.1"
[139] "Pp3c2_37190V3.1" "Pp3c2_37299V3.1" "Pp3c2_37670V3.1" "Pp3c2_38120V3.1" "Pp3c3_240V3.1" "Pp3c3_330V3.1"
[145] "Pp3c3_1164V3.1" "Pp3c3_1650V3.1" "Pp3c3_2130V3.1" "Pp3c3_2760V3.1" "Pp3c3_3070V3.1" "Pp3c3_4090V3.1"
[151] "Pp3c3_4970V3.1" "Pp3c3_5810V3.1" "Pp3c3_5930V3.1" "Pp3c3_6370V3.1" "Pp3c3_7020V3.1" "Pp3c3_7180V3.1"
[157] "Pp3c3_7440V3.1" "Pp3c3_8880V3.1" "Pp3c3_9200V3.1" "Pp3c3_10140V3.1" "Pp3c3_10250V3.1" "Pp3c3_10350V3.1"
[163] "Pp3c3_10730V3.1" "Pp3c3_11230V3.1" "Pp3c3_11730V3.1" "Pp3c3_11770V3.1" "Pp3c3_11840V3.1" "Pp3c3_11932V3.1"
[169] "Pp3c3_12090V3.1" "Pp3c3_12760V3.1" "Pp3c3_13220V3.1" "Pp3c3_13550V3.1" "Pp3c3_15040V3.1" "Pp3c3_16280V3.1"
[175] "Pp3c3_16880V3.1" "Pp3c3_17340V3.1" "Pp3c3_17950V3.1" "Pp3c3_18750V3.1" "Pp3c3_19510V3.1" "Pp3c3_19580V3.1"
[181] "Pp3c3_20390V3.1" "Pp3c3_21440V3.1" "Pp3c3_22090V3.1" "Pp3c3_22490V3.1" "Pp3c3_22750V3.1" "Pp3c3_22850V3.1"
[187] "Pp3c3_23410V3.1" "Pp3c3_23880V3.1" "Pp3c3_25110V3.1" "Pp3c3_25410V3.1" "Pp3c3_26950V3.1" "Pp3c3_28140V3.1"
[193] "Pp3c3_28810V3.1" "Pp3c3_29530V3.1" "Pp3c3_29970V3.1" "Pp3c3_30140V3.1" "Pp3c3_30150V3.1" "Pp3c3_30210V3.1"
[199] "Pp3c3_30710V3.1" "Pp3c3_30990V3.1" "Pp3c3_31900V3.1" "Pp3c3_32390V3.1" "Pp3c3_32490V3.1" "Pp3c3_32790V3.1"
[205] "Pp3c3_33400V3.1" "Pp3c3_34050V3.1" "Pp3c3_34790V3.1" "Pp3c3_35180V3.1" "Pp3c3_35850V3.1" "Pp3c3_37020V3.1"
[211] "Pp3c3_37260V3.1" "Pp3c3_38080V3.1" "Pp3c4_810V3.1" "Pp3c4_1020V3.1" "Pp3c4_1240V3.1" "Pp3c4_1450V3.1"
[217] "Pp3c4_1630V3.1" "Pp3c4_3650V3.1" "Pp3c4_3890V3.1" "Pp3c4_4420V3.1" "Pp3c4_4910V3.1" "Pp3c4_6260V3.1"
[223] "Pp3c4_6480V3.1" "Pp3c4_6590V3.1" "Pp3c4_6620V3.1" "Pp3c4_6870V3.1" "Pp3c4_7680V3.1" "Pp3c4_7960V3.1"
[229] "Pp3c4_8140V3.1" "Pp3c4_8171V3.1" "Pp3c4_8640V3.1" "Pp3c4_10120V3.1" "Pp3c4_11270V3.1" "Pp3c4_11854V3.1"
[235] "Pp3c4_13060V3.1" "Pp3c4_13280V3.1" "Pp3c4_15440V3.1" "Pp3c4_15860V3.1" "Pp3c4_16840V3.1" "Pp3c4_17890V3.1"
[241] "Pp3c4_17920V3.1" "Pp3c4_18160V3.1" "Pp3c4_20120V3.1" "Pp3c4_20700V3.1" "Pp3c4_21240V3.1" "Pp3c4_21630V3.1"
[247] "Pp3c4_22170V3.1" "Pp3c4_22180V3.1" "Pp3c4_22420V3.1" "Pp3c4_22490V3.1" "Pp3c4_22510V3.1" "Pp3c4_22810V3.1"
[253] "Pp3c4_23170V3.1" "Pp3c4_24130V3.1" "Pp3c4_26990V3.1" "Pp3c4_27460V3.1" "Pp3c4_28130V3.1" "Pp3c4_29200V3.1"
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[277] "Pp3c5_3160V3.1" "Pp3c5_3210V3.1" "Pp3c5_3300V3.1" "Pp3c5_3400V3.1" "Pp3c5_4200V3.1" "Pp3c5_4230V3.1"
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[289] "Pp3c5_8420V3.1" "Pp3c5_9550V3.1" "Pp3c5_9780V3.1" "Pp3c5_10250V3.1" "Pp3c5_10280V3.1" "Pp3c5_10320V3.1"
[295] "Pp3c5_10760V3.1" "Pp3c5_10920V3.1" "Pp3c5_10960V3.1" "Pp3c5_11200V3.1" "Pp3c5_11390V3.1" "Pp3c5_12950V3.1"
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[349] "Pp3c6_14810V3.1" "Pp3c6_15090V3.1" "Pp3c6_15900V3.1" "Pp3c6_16730V3.1" "Pp3c6_16970V3.1" "Pp3c6_17399V3.1"
[355] "Pp3c6_18400V3.1" "Pp3c6_18430V3.1" "Pp3c6_18880V3.1" "Pp3c6_19290V3.1" "Pp3c6_19730V3.1" "Pp3c6_20760V3.1"
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[367] "Pp3c6_23230V3.1" "Pp3c6_23280V3.1" "Pp3c6_24400V3.1" "Pp3c6_25090V3.1" "Pp3c6_25270V3.1" "Pp3c6_25660V3.1"
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[379] "Pp3c6_29630V3.1" "Pp3c7_80V3.1" "Pp3c7_1880V3.1" "Pp3c7_2440V3.1" "Pp3c7_2560V3.1" "Pp3c7_3910V3.1"
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[415] "Pp3c7_23810V3.1" "Pp3c7_23970V3.1" "Pp3c7_23980V3.1" "Pp3c7_24490V3.1" "Pp3c7_25080V3.1" "Pp3c7_26010V3.1"
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[445] "Pp3c8_13570V3.1" "Pp3c8_13930V3.1" "Pp3c8_15610V3.1" "Pp3c8_16740V3.1" "Pp3c8_16960V3.1" "Pp3c8_17140V3.1"
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[529] "Pp3c10_12250V3.1" "Pp3c10_12440V3.1" "Pp3c10_12450V3.1" "Pp3c10_13170V3.1" "Pp3c10_13610V3.1" "Pp3c10_14650V3.1"
[535] "Pp3c10_15520V3.1" "Pp3c10_15730V3.1" "Pp3c10_16080V3.1" "Pp3c10_16180V3.1" "Pp3c10_16560V3.1" "Pp3c10_17110V3.1"
[541] "Pp3c10_17120V3.1" "Pp3c10_18330V3.1" "Pp3c10_18860V3.1" "Pp3c10_19190V3.1" "Pp3c10_20060V3.1" "Pp3c10_20350V3.1"
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[787] "Pp3c16_7180V3.1" "Pp3c16_7660V3.1" "Pp3c16_8090V3.1" "Pp3c16_8260V3.1" "Pp3c16_8430V3.1" "Pp3c16_8500V3.1"
[793] "Pp3c16_8850V3.1" "Pp3c16_10460V3.1" "Pp3c16_11320V3.1" "Pp3c16_11630V3.1" "Pp3c16_11800V3.1" "Pp3c16_13700V3.1"
[799] "Pp3c16_14220V3.1" "Pp3c16_14400V3.1" "Pp3c16_15270V3.1" "Pp3c16_15860V3.1" "Pp3c16_16440V3.1" "Pp3c16_16680V3.1"
[805] "Pp3c16_17280V3.1" "Pp3c16_18590V3.1" "Pp3c16_18700V3.1" "Pp3c16_18710V3.1" "Pp3c16_19530V3.1" "Pp3c16_20890V3.1"
[811] "Pp3c16_21250V3.1" "Pp3c16_21900V3.1" "Pp3c16_22280V3.1" "Pp3c16_22330V3.1" "Pp3c16_22430V3.1" "Pp3c16_22550V3.1"
[817] "Pp3c16_22650V3.1" "Pp3c16_23230V3.1" "Pp3c16_24460V3.1" "Pp3c16_25600V3.1" "Pp3c16_25860V3.1" "Pp3c17_5070V3.1"
[823] "Pp3c17_5130V3.1" "Pp3c17_5320V3.1" "Pp3c17_5990V3.1" "Pp3c17_6090V3.1" "Pp3c17_7480V3.1" "Pp3c17_7560V3.1"
[829] "Pp3c17_7680V3.1" "Pp3c17_7790V3.1" "Pp3c17_9810V3.1" "Pp3c17_10170V3.1" "Pp3c17_12450V3.1" "Pp3c17_12980V3.1"
[835] "Pp3c17_13330V3.1" "Pp3c17_13940V3.1" "Pp3c17_14660V3.1" "Pp3c17_15380V3.1" "Pp3c17_15490V3.1" "Pp3c17_15920V3.1"
[841] "Pp3c17_16620V3.1" "Pp3c17_16790V3.1" "Pp3c17_17180V3.1" "Pp3c17_17840V3.1" "Pp3c17_19540V3.1" "Pp3c17_19570V3.1"
[847] "Pp3c17_20040V3.1" "Pp3c17_20310V3.1" "Pp3c17_21100V3.1" "Pp3c17_21120V3.1" "Pp3c17_21430V3.1" "Pp3c17_22200V3.1"
[853] "Pp3c17_23030V3.1" "Pp3c17_23180V3.1" "Pp3c17_23450V3.1" "Pp3c17_23740V3.1" "Pp3c17_24100V3.1" "Pp3c18_310V3.1"
[859] "Pp3c18_2170V3.1" "Pp3c18_3460V3.1" "Pp3c18_5680V3.1" "Pp3c18_5720V3.1" "Pp3c18_6179V3.1" "Pp3c18_6510V3.1"
[865] "Pp3c18_7740V3.1" "Pp3c18_7860V3.1" "Pp3c18_8240V3.1" "Pp3c18_8820V3.1" "Pp3c18_9820V3.1" "Pp3c18_9840V3.1"
[871] "Pp3c18_10760V3.1" "Pp3c18_10780V3.1" "Pp3c18_11000V3.1" "Pp3c18_13090V3.1" "Pp3c18_13570V3.1" "Pp3c18_14350V3.1"
[877] "Pp3c18_16700V3.1" "Pp3c18_18390V3.1" "Pp3c18_18460V3.1" "Pp3c18_18530V3.1" "Pp3c18_18670V3.1" "Pp3c18_19220V3.1"
[883] "Pp3c18_19690V3.1" "Pp3c18_19850V3.1" "Pp3c18_19990V3.1" "Pp3c18_20510V3.1" "Pp3c19_1490V3.1" "Pp3c19_1710V3.1"
[889] "Pp3c19_1760V3.1" "Pp3c19_2740V3.1" "Pp3c19_2860V3.1" "Pp3c19_3740V3.1" "Pp3c19_3750V3.1" "Pp3c19_4313V3.1"
[895] "Pp3c19_4500V3.1" "Pp3c19_4640V3.1" "Pp3c19_4900V3.1" "Pp3c19_5110V3.1" "Pp3c19_5510V3.1" "Pp3c19_6050V3.1"
[901] "Pp3c19_6670V3.1" "Pp3c19_6700V3.1" "Pp3c19_6710V3.1" "Pp3c19_7960V3.1" "Pp3c19_8330V3.1" "Pp3c19_8770V3.1"
[907] "Pp3c19_13170V3.1" "Pp3c19_14460V3.1" "Pp3c19_15500V3.1" "Pp3c19_15590V3.1" "Pp3c19_15790V3.1" "Pp3c19_15800V3.1"
[913] "Pp3c19_16810V3.1" "Pp3c19_17080V3.1" "Pp3c19_17290V3.1" "Pp3c19_19970V3.1" "Pp3c19_20160V3.1" "Pp3c19_20230V3.1"
[919] "Pp3c19_20270V3.1" "Pp3c19_20540V3.1" "Pp3c19_20720V3.1" "Pp3c19_20750V3.1" "Pp3c19_20780V3.1" "Pp3c19_20830V3.1"
[925] "Pp3c19_22410V3.1" "Pp3c20_1560V3.1" "Pp3c20_1800V3.1" "Pp3c20_1940V3.1" "Pp3c20_2280V3.1" "Pp3c20_2330V3.1"
[931] "Pp3c20_2890V3.1" "Pp3c20_2980V3.1" "Pp3c20_3610V3.1" "Pp3c20_3750V3.1" "Pp3c20_4670V3.1" "Pp3c20_5530V3.1"
[937] "Pp3c20_6430V3.1" "Pp3c20_7050V3.1" "Pp3c20_7850V3.1" "Pp3c20_7860V3.1" "Pp3c20_8330V3.1" "Pp3c20_9200V3.1"
[943] "Pp3c20_10210V3.1" "Pp3c20_10270V3.1" "Pp3c20_10460V3.1" "Pp3c20_10830V3.1" "Pp3c20_11000V3.1" "Pp3c20_12850V3.1"
[949] "Pp3c20_12980V3.1" "Pp3c20_14280V3.1" "Pp3c20_15780V3.1" "Pp3c20_16210V3.1" "Pp3c20_16950V3.1" "Pp3c20_17620V3.1"
[955] "Pp3c20_17800V3.1" "Pp3c20_17990V3.1" "Pp3c20_19960V3.1" "Pp3c20_21960V3.1" "Pp3c20_21990V3.1" "Pp3c20_22450V3.1"
[961] "Pp3c20_22760V3.1" "Pp3c20_22830V3.1" "Pp3c20_22890V3.1" "Pp3c20_23430V3.1" "Pp3c20_23560V3.1" "Pp3c21_180V3.1"
[967] "Pp3c21_1210V3.1" "Pp3c21_5070V3.1" "Pp3c21_5560V3.1" "Pp3c21_6150V3.1" "Pp3c21_6200V3.1" "Pp3c21_6390V3.1"
[973] "Pp3c21_6920V3.1" "Pp3c21_7810V3.1" "Pp3c21_8670V3.1" "Pp3c21_8940V3.1" "Pp3c21_9220V3.1" "Pp3c21_9380V3.1"
[979] "Pp3c21_9970V3.1" "Pp3c21_10000V3.1" "Pp3c21_10620V3.1" "Pp3c21_12100V3.1" "Pp3c21_12310V3.1" "Pp3c21_13720V3.1"
[985] "Pp3c21_14540V3.1" "Pp3c21_14830V3.1" "Pp3c21_15140V3.1" "Pp3c21_15660V3.1" "Pp3c21_16670V3.1" "Pp3c21_17930V3.1"
[991] "Pp3c21_18980V3.1" "Pp3c21_19760V3.1" "Pp3c21_21410V3.1" "Pp3c21_21800V3.1" "Pp3c22_1450V3.1" "Pp3c22_1930V3.1"
[997] "Pp3c22_3550V3.1" "Pp3c22_3910V3.1" "Pp3c22_4630V3.1" "Pp3c22_5470V3.1"
[ reached getOption("max.print") -- omitted 193 entries ]
[1] "DEGs edgeR"
[1] 5829
[1] "DEGs deseq2"
[1] 4265
[1] "DEGs noiseq"
[1] 1810
[1] "DEGs noiseqbio"
[1] 1704
[1] "DEGs intersection without direction check (three methods)"
[1] 1748
[1] "Pp3c1_100V3.1" "Pp3c1_200V3.1" "Pp3c1_470V3.1" "Pp3c1_540V3.1" "Pp3c1_690V3.1" "Pp3c1_1000V3.1"
[7] "Pp3c1_1870V3.1" "Pp3c1_1940V3.1" "Pp3c1_2420V3.1" "Pp3c1_3180V3.1" "Pp3c1_3200V3.1" "Pp3c1_3260V3.1"
[13] "Pp3c1_4180V3.1" "Pp3c1_4270V3.1" "Pp3c1_4400V3.1" "Pp3c1_4750V3.1" "Pp3c1_5050V3.1" "Pp3c1_5300V3.1"
[19] "Pp3c1_5870V3.1" "Pp3c1_6070V3.1" "Pp3c1_6110V3.1" "Pp3c1_6640V3.1" "Pp3c1_7370V3.1" "Pp3c1_7380V3.1"
[25] "Pp3c1_7540V3.1" "Pp3c1_7910V3.1" "Pp3c1_7950V3.1" "Pp3c1_8190V3.1" "Pp3c1_8490V3.1" "Pp3c1_9320V3.1"
[31] "Pp3c1_9560V3.1" "Pp3c1_10010V3.1" "Pp3c1_10180V3.1" "Pp3c1_10470V3.1" "Pp3c1_10540V3.1" "Pp3c1_10630V3.1"
[37] "Pp3c1_10970V3.1" "Pp3c1_11030V3.1" "Pp3c1_11190V3.1" "Pp3c1_12470V3.1" "Pp3c1_13170V3.1" "Pp3c1_13570V3.1"
[43] "Pp3c1_13910V3.1" "Pp3c1_15090V3.1" "Pp3c1_15150V3.1" "Pp3c1_15400V3.1" "Pp3c1_15410V3.1" "Pp3c1_15490V3.1"
[49] "Pp3c1_15690V3.1" "Pp3c1_16840V3.1" "Pp3c1_17080V3.1" "Pp3c1_17220V3.1" "Pp3c1_17860V3.1" "Pp3c1_18860V3.1"
[55] "Pp3c1_19060V3.1" "Pp3c1_19230V3.1" "Pp3c1_19370V3.1" "Pp3c1_20280V3.1" "Pp3c1_20430V3.1" "Pp3c1_20700V3.1"
[61] "Pp3c1_20980V3.1" "Pp3c1_21160V3.1" "Pp3c1_21400V3.1" "Pp3c1_21540V3.1" "Pp3c1_21890V3.1" "Pp3c1_22260V3.1"
[67] "Pp3c1_22450V3.1" "Pp3c1_23370V3.1" "Pp3c1_24000V3.1" "Pp3c1_24280V3.1" "Pp3c1_24500V3.1" "Pp3c1_24560V3.1"
[73] "Pp3c1_24790V3.1" "Pp3c1_25700V3.1" "Pp3c1_25770V3.1" "Pp3c1_25930V3.1" "Pp3c1_25980V3.1" "Pp3c1_26200V3.1"
[79] "Pp3c1_27270V3.1" "Pp3c1_27440V3.1" "Pp3c1_27510V3.1" "Pp3c1_27630V3.1" "Pp3c1_28390V3.1" "Pp3c1_29300V3.1"
[85] "Pp3c1_29630V3.1" "Pp3c1_29650V3.1" "Pp3c1_29700V3.1" "Pp3c1_30150V3.1" "Pp3c1_30410V3.1" "Pp3c1_30570V3.1"
[91] "Pp3c1_30660V3.1" "Pp3c1_30760V3.1" "Pp3c1_30790V3.1" "Pp3c1_31440V3.1" "Pp3c1_31540V3.1" "Pp3c1_31720V3.1"
[97] "Pp3c1_31850V3.1" "Pp3c1_32350V3.1" "Pp3c1_32810V3.1" "Pp3c1_32910V3.1" "Pp3c1_33050V3.1" "Pp3c1_33470V3.1"
[103] "Pp3c1_33480V3.1" "Pp3c1_33830V3.1" "Pp3c1_34890V3.1" "Pp3c1_35100V3.1" "Pp3c1_35330V3.1" "Pp3c1_35990V3.1"
[109] "Pp3c1_36100V3.1" "Pp3c1_36180V3.1" "Pp3c1_37110V3.1" "Pp3c1_38210V3.1" "Pp3c1_38250V3.1" "Pp3c1_38340V3.1"
[115] "Pp3c1_38440V3.1" "Pp3c1_38630V3.1" "Pp3c1_38880V3.1" "Pp3c1_39540V3.1" "Pp3c1_39640V3.1" "Pp3c1_39780V3.1"
[121] "Pp3c1_39990V3.1" "Pp3c1_40040V3.1" "Pp3c1_40610V3.1" "Pp3c1_40790V3.1" "Pp3c1_42020V3.1" "Pp3c2_181V3.1"
[127] "Pp3c2_200V3.1" "Pp3c2_1280V3.1" "Pp3c2_2120V3.1" "Pp3c2_2220V3.1" "Pp3c2_2520V3.1" "Pp3c2_2730V3.1"
[133] "Pp3c2_2760V3.1" "Pp3c2_2830V3.1" "Pp3c2_3490V3.1" "Pp3c2_4100V3.1" "Pp3c2_4500V3.1" "Pp3c2_4520V3.1"
[139] "Pp3c2_5280V3.1" "Pp3c2_6340V3.1" "Pp3c2_6410V3.1" "Pp3c2_6630V3.1" "Pp3c2_6690V3.1" "Pp3c2_6750V3.1"
[145] "Pp3c2_7120V3.1" "Pp3c2_8420V3.1" "Pp3c2_8660V3.1" "Pp3c2_9460V3.1" "Pp3c2_9920V3.1" "Pp3c2_10260V3.1"
[151] "Pp3c2_10380V3.1" "Pp3c2_10530V3.1" "Pp3c2_11190V3.1" "Pp3c2_12080V3.1" "Pp3c2_12150V3.1" "Pp3c2_12320V3.1"
[157] "Pp3c2_12680V3.1" "Pp3c2_13280V3.1" "Pp3c2_13330V3.1" "Pp3c2_13670V3.1" "Pp3c2_13990V3.1" "Pp3c2_14290V3.1"
[163] "Pp3c2_14400V3.1" "Pp3c2_14600V3.1" "Pp3c2_15140V3.1" "Pp3c2_15400V3.1" "Pp3c2_16030V3.1" "Pp3c2_17110V3.1"
[169] "Pp3c2_17290V3.1" "Pp3c2_17450V3.1" "Pp3c2_17670V3.1" "Pp3c2_17700V3.1" "Pp3c2_18130V3.1" "Pp3c2_19610V3.1"
[175] "Pp3c2_20160V3.1" "Pp3c2_20450V3.1" "Pp3c2_20840V3.1" "Pp3c2_21670V3.1" "Pp3c2_21970V3.1" "Pp3c2_22000V3.1"
[181] "Pp3c2_22140V3.1" "Pp3c2_22630V3.1" "Pp3c2_23590V3.1" "Pp3c2_23900V3.1" "Pp3c2_24160V3.1" "Pp3c2_24620V3.1"
[187] "Pp3c2_25720V3.1" "Pp3c2_25890V3.1" "Pp3c2_26060V3.1" "Pp3c2_26270V3.1" "Pp3c2_28030V3.1" "Pp3c2_29140V3.1"
[193] "Pp3c2_29420V3.1" "Pp3c2_29720V3.1" "Pp3c2_30230V3.1" "Pp3c2_30630V3.1" "Pp3c2_30860V3.1" "Pp3c2_30980V3.1"
[199] "Pp3c2_32540V3.1" "Pp3c2_32690V3.1" "Pp3c2_32770V3.1" "Pp3c2_33890V3.1" "Pp3c2_34310V3.1" "Pp3c2_34390V3.1"
[205] "Pp3c2_34670V3.1" "Pp3c2_35010V3.1" "Pp3c2_35740V3.1" "Pp3c2_35950V3.1" "Pp3c2_36790V3.1" "Pp3c2_36940V3.1"
[211] "Pp3c2_37190V3.1" "Pp3c2_37299V3.1" "Pp3c2_37670V3.1" "Pp3c2_38120V3.1" "Pp3c3_240V3.1" "Pp3c3_330V3.1"
[217] "Pp3c3_810V3.1" "Pp3c3_1164V3.1" "Pp3c3_1650V3.1" "Pp3c3_2130V3.1" "Pp3c3_2240V3.1" "Pp3c3_2760V3.1"
[223] "Pp3c3_3070V3.1" "Pp3c3_4090V3.1" "Pp3c3_4970V3.1" "Pp3c3_5570V3.1" "Pp3c3_5810V3.1" "Pp3c3_5930V3.1"
[229] "Pp3c3_6370V3.1" "Pp3c3_7020V3.1" "Pp3c3_7160V3.1" "Pp3c3_7180V3.1" "Pp3c3_7440V3.1" "Pp3c3_8880V3.1"
[235] "Pp3c3_9200V3.1" "Pp3c3_9650V3.1" "Pp3c3_10140V3.1" "Pp3c3_10250V3.1" "Pp3c3_10350V3.1" "Pp3c3_10730V3.1"
[241] "Pp3c3_11230V3.1" "Pp3c3_11730V3.1" "Pp3c3_11770V3.1" "Pp3c3_11840V3.1" "Pp3c3_11932V3.1" "Pp3c3_11940V3.1"
[247] "Pp3c3_12090V3.1" "Pp3c3_12760V3.1" "Pp3c3_13220V3.1" "Pp3c3_13550V3.1" "Pp3c3_13660V3.1" "Pp3c3_15040V3.1"
[253] "Pp3c3_15330V3.1" "Pp3c3_15560V3.1" "Pp3c3_16150V3.1" "Pp3c3_16280V3.1" "Pp3c3_16880V3.1" "Pp3c3_17340V3.1"
[259] "Pp3c3_17950V3.1" "Pp3c3_18750V3.1" "Pp3c3_18760V3.1" "Pp3c3_19510V3.1" "Pp3c3_19580V3.1" "Pp3c3_19590V3.1"
[265] "Pp3c3_19970V3.1" "Pp3c3_20390V3.1" "Pp3c3_20740V3.1" "Pp3c3_21440V3.1" "Pp3c3_22090V3.1" "Pp3c3_22420V3.1"
[271] "Pp3c3_22490V3.1" "Pp3c3_22750V3.1" "Pp3c3_22850V3.1" "Pp3c3_23410V3.1" "Pp3c3_23880V3.1" "Pp3c3_24530V3.1"
[277] "Pp3c3_24970V3.1" "Pp3c3_25110V3.1" "Pp3c3_25210V3.1" "Pp3c3_25410V3.1" "Pp3c3_26310V3.1" "Pp3c3_26910V3.1"
[283] "Pp3c3_26940V3.1" "Pp3c3_26950V3.1" "Pp3c3_28000V3.1" "Pp3c3_28140V3.1" "Pp3c3_28300V3.1" "Pp3c3_28810V3.1"
[289] "Pp3c3_29330V3.1" "Pp3c3_29480V3.1" "Pp3c3_29530V3.1" "Pp3c3_29970V3.1" "Pp3c3_30120V3.1" "Pp3c3_30140V3.1"
[295] "Pp3c3_30150V3.1" "Pp3c3_30210V3.1" "Pp3c3_30710V3.1" "Pp3c3_30990V3.1" "Pp3c3_31900V3.1" "Pp3c3_32100V3.1"
[301] "Pp3c3_32390V3.1" "Pp3c3_32490V3.1" "Pp3c3_32650V3.1" "Pp3c3_32790V3.1" "Pp3c3_33400V3.1" "Pp3c3_34050V3.1"
[307] "Pp3c3_34440V3.1" "Pp3c3_34790V3.1" "Pp3c3_35020V3.1" "Pp3c3_35180V3.1" "Pp3c3_35850V3.1" "Pp3c3_37020V3.1"
[313] "Pp3c3_37260V3.1" "Pp3c3_37400V3.1" "Pp3c3_38080V3.1" "Pp3c4_810V3.1" "Pp3c4_1020V3.1" "Pp3c4_1240V3.1"
[319] "Pp3c4_1450V3.1" "Pp3c4_1630V3.1" "Pp3c4_3420V3.1" "Pp3c4_3550V3.1" "Pp3c4_3650V3.1" "Pp3c4_3730V3.1"
[325] "Pp3c4_3890V3.1" "Pp3c4_3930V3.1" "Pp3c4_4420V3.1" "Pp3c4_4910V3.1" "Pp3c4_6260V3.1" "Pp3c4_6340V3.1"
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[859] "Pp3c11_23950V3.1" "Pp3c11_24020V3.1" "Pp3c11_24130V3.1" "Pp3c11_24200V3.1" "Pp3c11_24210V3.1" "Pp3c11_24300V3.1"
[865] "Pp3c11_24520V3.1" "Pp3c11_25550V3.1" "Pp3c11_25720V3.1" "Pp3c11_26420V3.1" "Pp3c11_26700V3.1" "Pp3c12_1270V3.1"
[871] "Pp3c12_1790V3.1" "Pp3c12_2220V3.1" "Pp3c12_2540V3.1" "Pp3c12_4490V3.1" "Pp3c12_4540V3.1" "Pp3c12_4580V3.1"
[877] "Pp3c12_5220V3.1" "Pp3c12_5490V3.1" "Pp3c12_5540V3.1" "Pp3c12_6520V3.1" "Pp3c12_6700V3.1" "Pp3c12_7010V3.1"
[883] "Pp3c12_8850V3.1" "Pp3c12_9890V3.1" "Pp3c12_10890V3.1" "Pp3c12_11350V3.1" "Pp3c12_11600V3.1" "Pp3c12_11700V3.1"
[889] "Pp3c12_11880V3.1" "Pp3c12_12500V3.1" "Pp3c12_13650V3.1" "Pp3c12_13870V3.1" "Pp3c12_14020V3.1" "Pp3c12_14130V3.1"
[895] "Pp3c12_14210V3.1" "Pp3c12_15000V3.1" "Pp3c12_16890V3.1" "Pp3c12_17320V3.1" "Pp3c12_17430V3.1" "Pp3c12_19200V3.1"
[901] "Pp3c12_20650V3.1" "Pp3c12_21300V3.1" "Pp3c12_22390V3.1" "Pp3c12_22440V3.1" "Pp3c12_22830V3.1" "Pp3c12_22890V3.1"
[907] "Pp3c12_22970V3.1" "Pp3c12_22990V3.1" "Pp3c12_23650V3.1" "Pp3c12_23720V3.1" "Pp3c12_23930V3.1" "Pp3c12_24350V3.1"
[913] "Pp3c12_24950V3.1" "Pp3c12_24970V3.1" "Pp3c12_25380V3.1" "Pp3c12_25460V3.1" "Pp3c12_25580V3.1" "Pp3c12_25760V3.1"
[919] "Pp3c12_25900V3.1" "Pp3c12_25950V3.1" "Pp3c12_26230V3.1" "Pp3c13_300V3.1" "Pp3c13_910V3.1" "Pp3c13_970V3.1"
[925] "Pp3c13_1900V3.1" "Pp3c13_2000V3.1" "Pp3c13_3830V3.1" "Pp3c13_4250V3.1" "Pp3c13_4300V3.1" "Pp3c13_4380V3.1"
[931] "Pp3c13_5750V3.1" "Pp3c13_6290V3.1" "Pp3c13_6760V3.1" "Pp3c13_6860V3.1" "Pp3c13_7070V3.1" "Pp3c13_7390V3.1"
[937] "Pp3c13_8480V3.1" "Pp3c13_8540V3.1" "Pp3c13_8750V3.1" "Pp3c13_8810V3.1" "Pp3c13_10330V3.1" "Pp3c13_10500V3.1"
[943] "Pp3c13_10560V3.1" "Pp3c13_11160V3.1" "Pp3c13_11470V3.1" "Pp3c13_11750V3.1" "Pp3c13_11800V3.1" "Pp3c13_12000V3.1"
[949] "Pp3c13_12390V3.1" "Pp3c13_12420V3.1" "Pp3c13_12570V3.1" "Pp3c13_12640V3.1" "Pp3c13_13170V3.1" "Pp3c13_13839V3.1"
[955] "Pp3c13_13852V3.1" "Pp3c13_15150V3.1" "Pp3c13_15520V3.1" "Pp3c13_15600V3.1" "Pp3c13_16600V3.1" "Pp3c13_16620V3.1"
[961] "Pp3c13_16630V3.1" "Pp3c13_18500V3.1" "Pp3c13_18510V3.1" "Pp3c13_19960V3.1" "Pp3c13_20140V3.1" "Pp3c13_20360V3.1"
[967] "Pp3c13_20640V3.1" "Pp3c13_21311V3.1" "Pp3c13_21410V3.1" "Pp3c13_22230V3.1" "Pp3c13_22390V3.1" "Pp3c13_22750V3.1"
[973] "Pp3c13_23280V3.1" "Pp3c13_23600V3.1" "Pp3c13_23730V3.1" "Pp3c13_24510V3.1" "Pp3c13_24520V3.1" "Pp3c14_380V3.1"
[979] "Pp3c14_2990V3.1" "Pp3c14_3670V3.1" "Pp3c14_3770V3.1" "Pp3c14_4330V3.1" "Pp3c14_5560V3.1" "Pp3c14_5600V3.1"
[985] "Pp3c14_6030V3.1" "Pp3c14_6070V3.1" "Pp3c14_6110V3.1" "Pp3c14_6120V3.1" "Pp3c14_6150V3.1" "Pp3c14_6380V3.1"
[991] "Pp3c14_6650V3.1" "Pp3c14_7160V3.1" "Pp3c14_7960V3.1" "Pp3c14_8480V3.1" "Pp3c14_8590V3.1" "Pp3c14_8650V3.1"
[997] "Pp3c14_8740V3.1" "Pp3c14_8940V3.1" "Pp3c14_9100V3.1" "Pp3c14_9580V3.1"
[ reached getOption("max.print") -- omitted 748 entries ]
[1] "DEGs intersection with direction check"
[1] 1748
[1] "Pp3c1_100V3.1" "Pp3c1_200V3.1" "Pp3c1_470V3.1" "Pp3c1_540V3.1" "Pp3c1_690V3.1" "Pp3c1_1000V3.1"
[7] "Pp3c1_1870V3.1" "Pp3c1_1940V3.1" "Pp3c1_2420V3.1" "Pp3c1_3180V3.1" "Pp3c1_3200V3.1" "Pp3c1_3260V3.1"
[13] "Pp3c1_4180V3.1" "Pp3c1_4270V3.1" "Pp3c1_4400V3.1" "Pp3c1_4750V3.1" "Pp3c1_5050V3.1" "Pp3c1_5300V3.1"
[19] "Pp3c1_5870V3.1" "Pp3c1_6070V3.1" "Pp3c1_6110V3.1" "Pp3c1_6640V3.1" "Pp3c1_7370V3.1" "Pp3c1_7380V3.1"
[25] "Pp3c1_7540V3.1" "Pp3c1_7910V3.1" "Pp3c1_7950V3.1" "Pp3c1_8190V3.1" "Pp3c1_8490V3.1" "Pp3c1_9320V3.1"
[31] "Pp3c1_9560V3.1" "Pp3c1_10010V3.1" "Pp3c1_10180V3.1" "Pp3c1_10470V3.1" "Pp3c1_10540V3.1" "Pp3c1_10630V3.1"
[37] "Pp3c1_10970V3.1" "Pp3c1_11030V3.1" "Pp3c1_11190V3.1" "Pp3c1_12470V3.1" "Pp3c1_13170V3.1" "Pp3c1_13570V3.1"
[43] "Pp3c1_13910V3.1" "Pp3c1_15090V3.1" "Pp3c1_15150V3.1" "Pp3c1_15400V3.1" "Pp3c1_15410V3.1" "Pp3c1_15490V3.1"
[49] "Pp3c1_15690V3.1" "Pp3c1_16840V3.1" "Pp3c1_17080V3.1" "Pp3c1_17220V3.1" "Pp3c1_17860V3.1" "Pp3c1_18860V3.1"
[55] "Pp3c1_19060V3.1" "Pp3c1_19230V3.1" "Pp3c1_19370V3.1" "Pp3c1_20280V3.1" "Pp3c1_20430V3.1" "Pp3c1_20700V3.1"
[61] "Pp3c1_20980V3.1" "Pp3c1_21160V3.1" "Pp3c1_21400V3.1" "Pp3c1_21540V3.1" "Pp3c1_21890V3.1" "Pp3c1_22260V3.1"
[67] "Pp3c1_22450V3.1" "Pp3c1_23370V3.1" "Pp3c1_24000V3.1" "Pp3c1_24280V3.1" "Pp3c1_24500V3.1" "Pp3c1_24560V3.1"
[73] "Pp3c1_24790V3.1" "Pp3c1_25700V3.1" "Pp3c1_25770V3.1" "Pp3c1_25930V3.1" "Pp3c1_25980V3.1" "Pp3c1_26200V3.1"
[79] "Pp3c1_27270V3.1" "Pp3c1_27440V3.1" "Pp3c1_27510V3.1" "Pp3c1_27630V3.1" "Pp3c1_28390V3.1" "Pp3c1_29300V3.1"
[85] "Pp3c1_29630V3.1" "Pp3c1_29650V3.1" "Pp3c1_29700V3.1" "Pp3c1_30150V3.1" "Pp3c1_30410V3.1" "Pp3c1_30570V3.1"
[91] "Pp3c1_30660V3.1" "Pp3c1_30760V3.1" "Pp3c1_30790V3.1" "Pp3c1_31440V3.1" "Pp3c1_31540V3.1" "Pp3c1_31720V3.1"
[97] "Pp3c1_31850V3.1" "Pp3c1_32350V3.1" "Pp3c1_32810V3.1" "Pp3c1_32910V3.1" "Pp3c1_33050V3.1" "Pp3c1_33470V3.1"
[103] "Pp3c1_33480V3.1" "Pp3c1_33830V3.1" "Pp3c1_34890V3.1" "Pp3c1_35100V3.1" "Pp3c1_35330V3.1" "Pp3c1_35990V3.1"
[109] "Pp3c1_36100V3.1" "Pp3c1_36180V3.1" "Pp3c1_37110V3.1" "Pp3c1_38210V3.1" "Pp3c1_38250V3.1" "Pp3c1_38340V3.1"
[115] "Pp3c1_38440V3.1" "Pp3c1_38630V3.1" "Pp3c1_38880V3.1" "Pp3c1_39540V3.1" "Pp3c1_39640V3.1" "Pp3c1_39780V3.1"
[121] "Pp3c1_39990V3.1" "Pp3c1_40040V3.1" "Pp3c1_40610V3.1" "Pp3c1_40790V3.1" "Pp3c1_42020V3.1" "Pp3c2_181V3.1"
[127] "Pp3c2_200V3.1" "Pp3c2_1280V3.1" "Pp3c2_2120V3.1" "Pp3c2_2220V3.1" "Pp3c2_2520V3.1" "Pp3c2_2730V3.1"
[133] "Pp3c2_2760V3.1" "Pp3c2_2830V3.1" "Pp3c2_3490V3.1" "Pp3c2_4100V3.1" "Pp3c2_4500V3.1" "Pp3c2_4520V3.1"
[139] "Pp3c2_5280V3.1" "Pp3c2_6340V3.1" "Pp3c2_6410V3.1" "Pp3c2_6630V3.1" "Pp3c2_6690V3.1" "Pp3c2_6750V3.1"
[145] "Pp3c2_7120V3.1" "Pp3c2_8420V3.1" "Pp3c2_8660V3.1" "Pp3c2_9460V3.1" "Pp3c2_9920V3.1" "Pp3c2_10260V3.1"
[151] "Pp3c2_10380V3.1" "Pp3c2_10530V3.1" "Pp3c2_11190V3.1" "Pp3c2_12080V3.1" "Pp3c2_12150V3.1" "Pp3c2_12320V3.1"
[157] "Pp3c2_12680V3.1" "Pp3c2_13280V3.1" "Pp3c2_13330V3.1" "Pp3c2_13670V3.1" "Pp3c2_13990V3.1" "Pp3c2_14290V3.1"
[163] "Pp3c2_14400V3.1" "Pp3c2_14600V3.1" "Pp3c2_15140V3.1" "Pp3c2_15400V3.1" "Pp3c2_16030V3.1" "Pp3c2_17110V3.1"
[169] "Pp3c2_17290V3.1" "Pp3c2_17450V3.1" "Pp3c2_17670V3.1" "Pp3c2_17700V3.1" "Pp3c2_18130V3.1" "Pp3c2_19610V3.1"
[175] "Pp3c2_20160V3.1" "Pp3c2_20450V3.1" "Pp3c2_20840V3.1" "Pp3c2_21670V3.1" "Pp3c2_21970V3.1" "Pp3c2_22000V3.1"
[181] "Pp3c2_22140V3.1" "Pp3c2_22630V3.1" "Pp3c2_23590V3.1" "Pp3c2_23900V3.1" "Pp3c2_24160V3.1" "Pp3c2_24620V3.1"
[187] "Pp3c2_25720V3.1" "Pp3c2_25890V3.1" "Pp3c2_26060V3.1" "Pp3c2_26270V3.1" "Pp3c2_28030V3.1" "Pp3c2_29140V3.1"
[193] "Pp3c2_29420V3.1" "Pp3c2_29720V3.1" "Pp3c2_30230V3.1" "Pp3c2_30630V3.1" "Pp3c2_30860V3.1" "Pp3c2_30980V3.1"
[199] "Pp3c2_32540V3.1" "Pp3c2_32690V3.1" "Pp3c2_32770V3.1" "Pp3c2_33890V3.1" "Pp3c2_34310V3.1" "Pp3c2_34390V3.1"
[205] "Pp3c2_34670V3.1" "Pp3c2_35010V3.1" "Pp3c2_35740V3.1" "Pp3c2_35950V3.1" "Pp3c2_36790V3.1" "Pp3c2_36940V3.1"
[211] "Pp3c2_37190V3.1" "Pp3c2_37299V3.1" "Pp3c2_37670V3.1" "Pp3c2_38120V3.1" "Pp3c3_240V3.1" "Pp3c3_330V3.1"
[217] "Pp3c3_810V3.1" "Pp3c3_1164V3.1" "Pp3c3_1650V3.1" "Pp3c3_2130V3.1" "Pp3c3_2240V3.1" "Pp3c3_2760V3.1"
[223] "Pp3c3_3070V3.1" "Pp3c3_4090V3.1" "Pp3c3_4970V3.1" "Pp3c3_5570V3.1" "Pp3c3_5810V3.1" "Pp3c3_5930V3.1"
[229] "Pp3c3_6370V3.1" "Pp3c3_7020V3.1" "Pp3c3_7160V3.1" "Pp3c3_7180V3.1" "Pp3c3_7440V3.1" "Pp3c3_8880V3.1"
[235] "Pp3c3_9200V3.1" "Pp3c3_9650V3.1" "Pp3c3_10140V3.1" "Pp3c3_10250V3.1" "Pp3c3_10350V3.1" "Pp3c3_10730V3.1"
[241] "Pp3c3_11230V3.1" "Pp3c3_11730V3.1" "Pp3c3_11770V3.1" "Pp3c3_11840V3.1" "Pp3c3_11932V3.1" "Pp3c3_11940V3.1"
[247] "Pp3c3_12090V3.1" "Pp3c3_12760V3.1" "Pp3c3_13220V3.1" "Pp3c3_13550V3.1" "Pp3c3_13660V3.1" "Pp3c3_15040V3.1"
[253] "Pp3c3_15330V3.1" "Pp3c3_15560V3.1" "Pp3c3_16150V3.1" "Pp3c3_16280V3.1" "Pp3c3_16880V3.1" "Pp3c3_17340V3.1"
[259] "Pp3c3_17950V3.1" "Pp3c3_18750V3.1" "Pp3c3_18760V3.1" "Pp3c3_19510V3.1" "Pp3c3_19580V3.1" "Pp3c3_19590V3.1"
[265] "Pp3c3_19970V3.1" "Pp3c3_20390V3.1" "Pp3c3_20740V3.1" "Pp3c3_21440V3.1" "Pp3c3_22090V3.1" "Pp3c3_22420V3.1"
[271] "Pp3c3_22490V3.1" "Pp3c3_22750V3.1" "Pp3c3_22850V3.1" "Pp3c3_23410V3.1" "Pp3c3_23880V3.1" "Pp3c3_24530V3.1"
[277] "Pp3c3_24970V3.1" "Pp3c3_25110V3.1" "Pp3c3_25210V3.1" "Pp3c3_25410V3.1" "Pp3c3_26310V3.1" "Pp3c3_26910V3.1"
[283] "Pp3c3_26940V3.1" "Pp3c3_26950V3.1" "Pp3c3_28000V3.1" "Pp3c3_28140V3.1" "Pp3c3_28300V3.1" "Pp3c3_28810V3.1"
[289] "Pp3c3_29330V3.1" "Pp3c3_29480V3.1" "Pp3c3_29530V3.1" "Pp3c3_29970V3.1" "Pp3c3_30120V3.1" "Pp3c3_30140V3.1"
[295] "Pp3c3_30150V3.1" "Pp3c3_30210V3.1" "Pp3c3_30710V3.1" "Pp3c3_30990V3.1" "Pp3c3_31900V3.1" "Pp3c3_32100V3.1"
[301] "Pp3c3_32390V3.1" "Pp3c3_32490V3.1" "Pp3c3_32650V3.1" "Pp3c3_32790V3.1" "Pp3c3_33400V3.1" "Pp3c3_34050V3.1"
[307] "Pp3c3_34440V3.1" "Pp3c3_34790V3.1" "Pp3c3_35020V3.1" "Pp3c3_35180V3.1" "Pp3c3_35850V3.1" "Pp3c3_37020V3.1"
[313] "Pp3c3_37260V3.1" "Pp3c3_37400V3.1" "Pp3c3_38080V3.1" "Pp3c4_810V3.1" "Pp3c4_1020V3.1" "Pp3c4_1240V3.1"
[319] "Pp3c4_1450V3.1" "Pp3c4_1630V3.1" "Pp3c4_3420V3.1" "Pp3c4_3550V3.1" "Pp3c4_3650V3.1" "Pp3c4_3730V3.1"
[325] "Pp3c4_3890V3.1" "Pp3c4_3930V3.1" "Pp3c4_4420V3.1" "Pp3c4_4910V3.1" "Pp3c4_6260V3.1" "Pp3c4_6340V3.1"
[331] "Pp3c4_6480V3.1" "Pp3c4_6590V3.1" "Pp3c4_6620V3.1" "Pp3c4_6770V3.1" "Pp3c4_6870V3.1" "Pp3c4_7080V3.1"
[337] "Pp3c4_7680V3.1" "Pp3c4_7870V3.1" "Pp3c4_7960V3.1" "Pp3c4_8130V3.1" "Pp3c4_8140V3.1" "Pp3c4_8171V3.1"
[343] "Pp3c4_8350V3.1" "Pp3c4_8640V3.1" "Pp3c4_10120V3.1" "Pp3c4_10760V3.1" "Pp3c4_11270V3.1" "Pp3c4_11854V3.1"
[349] "Pp3c4_13060V3.1" "Pp3c4_13280V3.1" "Pp3c4_13850V3.1" "Pp3c4_13980V3.1" "Pp3c4_15230V3.1" "Pp3c4_15440V3.1"
[355] "Pp3c4_15860V3.1" "Pp3c4_16840V3.1" "Pp3c4_17160V3.1" "Pp3c4_17670V3.1" "Pp3c4_17890V3.1" "Pp3c4_17920V3.1"
[361] "Pp3c4_18160V3.1" "Pp3c4_20120V3.1" "Pp3c4_20340V3.1" "Pp3c4_20400V3.1" "Pp3c4_20700V3.1" "Pp3c4_21240V3.1"
[367] "Pp3c4_21630V3.1" "Pp3c4_22100V3.1" "Pp3c4_22170V3.1" "Pp3c4_22180V3.1" "Pp3c4_22420V3.1" "Pp3c4_22490V3.1"
[373] "Pp3c4_22500V3.1" "Pp3c4_22510V3.1" "Pp3c4_22810V3.1" "Pp3c4_23170V3.1" "Pp3c4_24130V3.1" "Pp3c4_26000V3.1"
[379] "Pp3c4_26900V3.1" "Pp3c4_26990V3.1" "Pp3c4_27460V3.1" "Pp3c4_28130V3.1" "Pp3c4_28860V3.1" "Pp3c4_29200V3.1"
[385] "Pp3c4_29750V3.1" "Pp3c4_29920V3.1" "Pp3c4_30040V3.1" "Pp3c4_30220V3.1" "Pp3c4_30530V3.1" "Pp3c4_30547V3.1"
[391] "Pp3c4_30740V3.1" "Pp3c4_30860V3.1" "Pp3c4_30870V3.1" "Pp3c4_30950V3.1" "Pp3c4_31590V3.1" "Pp3c4_31800V3.1"
[397] "Pp3c4_32160V3.1" "Pp3c4_32350V3.1" "Pp3c5_200V3.1" "Pp3c5_640V3.1" "Pp3c5_1250V3.1" "Pp3c5_1370V3.1"
[403] "Pp3c5_1480V3.1" "Pp3c5_1630V3.1" "Pp3c5_2190V3.1" "Pp3c5_2850V3.1" "Pp3c5_3150V3.1" "Pp3c5_3160V3.1"
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[937] "Pp3c13_8480V3.1" "Pp3c13_8540V3.1" "Pp3c13_8750V3.1" "Pp3c13_8810V3.1" "Pp3c13_10330V3.1" "Pp3c13_10500V3.1"
[943] "Pp3c13_10560V3.1" "Pp3c13_11160V3.1" "Pp3c13_11470V3.1" "Pp3c13_11750V3.1" "Pp3c13_11800V3.1" "Pp3c13_12000V3.1"
[949] "Pp3c13_12390V3.1" "Pp3c13_12420V3.1" "Pp3c13_12570V3.1" "Pp3c13_12640V3.1" "Pp3c13_13170V3.1" "Pp3c13_13839V3.1"
[955] "Pp3c13_13852V3.1" "Pp3c13_15150V3.1" "Pp3c13_15520V3.1" "Pp3c13_15600V3.1" "Pp3c13_16600V3.1" "Pp3c13_16620V3.1"
[961] "Pp3c13_16630V3.1" "Pp3c13_18500V3.1" "Pp3c13_18510V3.1" "Pp3c13_19960V3.1" "Pp3c13_20140V3.1" "Pp3c13_20360V3.1"
[967] "Pp3c13_20640V3.1" "Pp3c13_21311V3.1" "Pp3c13_21410V3.1" "Pp3c13_22230V3.1" "Pp3c13_22390V3.1" "Pp3c13_22750V3.1"
[973] "Pp3c13_23280V3.1" "Pp3c13_23600V3.1" "Pp3c13_23730V3.1" "Pp3c13_24510V3.1" "Pp3c13_24520V3.1" "Pp3c14_380V3.1"
[979] "Pp3c14_2990V3.1" "Pp3c14_3670V3.1" "Pp3c14_3770V3.1" "Pp3c14_4330V3.1" "Pp3c14_5560V3.1" "Pp3c14_5600V3.1"
[985] "Pp3c14_6030V3.1" "Pp3c14_6070V3.1" "Pp3c14_6110V3.1" "Pp3c14_6120V3.1" "Pp3c14_6150V3.1" "Pp3c14_6380V3.1"
[991] "Pp3c14_6650V3.1" "Pp3c14_7160V3.1" "Pp3c14_7960V3.1" "Pp3c14_8480V3.1" "Pp3c14_8590V3.1" "Pp3c14_8650V3.1"
[997] "Pp3c14_8740V3.1" "Pp3c14_8940V3.1" "Pp3c14_9100V3.1" "Pp3c14_9580V3.1"
[ reached getOption("max.print") -- omitted 748 entries ]
runs/RNA-Seq_analysis/DEGs/DEGs_0.9/cop_L_WT_L/DESeq2/cop_L vs. WT_L_4265_DESeq2_fdr.tsv 0 → 100755
View file @ 8ebefab1
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