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runs/RNA-Seq_analysis/DEGs/31315.p.sort.counts 0 → 100755
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runs/RNA-Seq_analysis/DEGs/31315.p.sort.rpkm 0 → 100755
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runs/RNA-Seq_analysis/DEGs/31315.p.sort.wo_zero.counts 0 → 100755
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runs/RNA-Seq_analysis/DEGs/31315.p.sort.wo_zero.rpkm 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/WT_D_WT_L/DEGpipe_WT_D 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: WT_D" "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] "WT_D" "WT_D.1" "WT_D.2" "WT_L" "WT_L.1" "WT_L.2"
WT_D WT_D.1 WT_D.2 WT_L WT_L.1 WT_L.2
Pp3c1_20V3.1 194 198 298 299 421 446
Pp3c1_40V3.1 439 523 588 210 341 331
Pp3c1_60V3.1 622 626 743 339 533 550
Pp3c1_70V3.1 459 526 643 307 441 445
Pp3c1_80V3.1 1 1 0 0 0 0
Pp3c1_100V3.1 576 539 761 695 981 980
[1] "Raw data row number: 31315"
[1] "Raw data column number: 6"
[1] "Filtered data row number: 19626"
[1] "Filtered data row number: 6"
[1] "edgeR is running with WT_D vs. WT_L"
[1] "DESeq2 is running with WT_D vs. WT_L"
[1] "NOISeq is running with WT_D vs. WT_L"
Filtering out low count features...
18821 features are to be kept for differential expression analysis with filtering method 1
[1] "GC content bias detection is to be computed for:"
[1] "WT_D" "WT_D.1" "WT_D.2" "WT_L" "WT_L.1" "WT_L.2"
[1] "WT_D"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-86.871 -21.744 -0.207 19.491 85.657
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 249.76 34.56 7.227 2.09e-10 ***
bx1 -165.91 48.88 -3.394 0.00105 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 1275.37 4679.68 0.273 0.78588
bx5 -247.67 202.60 -1.222 0.22495
bx6 -64.19 52.30 -1.227 0.22308
bx7 130.34 39.65 3.287 0.00148 **
bx8 165.34 40.06 4.127 8.61e-05 ***
bx9 66.28 50.32 1.317 0.19141
bx10 53.61 146.80 0.365 0.71592
bx11 -602.49 796.55 -0.756 0.45154
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 34.56 on 84 degrees of freedom
Multiple R-squared: 0.7779, Adjusted R-squared: 0.7541
F-statistic: 32.69 on 9 and 84 DF, p-value: < 2.2e-16
[1] "WT_D.1"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-96.375 -24.544 -0.882 22.287 97.602
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 274.84 37.95 7.243 1.94e-10 ***
bx1 -181.39 53.67 -3.380 0.001102 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 1179.33 5138.34 0.230 0.819027
bx5 -258.49 222.46 -1.162 0.248547
bx6 -63.33 57.42 -1.103 0.273199
bx7 142.98 43.53 3.284 0.001492 **
bx8 179.09 43.99 4.071 0.000105 ***
bx9 66.49 55.26 1.203 0.232255
bx10 65.23 161.19 0.405 0.686768
bx11 -681.66 874.62 -0.779 0.437947
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 37.95 on 84 degrees of freedom
Multiple R-squared: 0.7681, Adjusted R-squared: 0.7432
F-statistic: 30.91 on 9 and 84 DF, p-value: < 2.2e-16
[1] "WT_D.2"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-114.489 -28.475 -2.787 24.050 120.103
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 281.54 44.27 6.360 1.01e-08 ***
bx1 -179.73 62.60 -2.871 0.00518 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 1694.60 5994.06 0.283 0.77809
bx5 -281.33 259.51 -1.084 0.28143
bx6 -25.81 66.99 -0.385 0.70100
bx7 217.01 50.78 4.273 5.06e-05 ***
bx8 270.00 51.31 5.262 1.07e-06 ***
bx9 134.18 64.46 2.082 0.04042 *
bx10 56.92 188.04 0.303 0.76285
bx11 -650.43 1020.28 -0.637 0.52553
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 44.27 on 84 degrees of freedom
Multiple R-squared: 0.7934, Adjusted R-squared: 0.7713
F-statistic: 35.85 on 9 and 84 DF, p-value: < 2.2e-16
[1] "WT_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-103.655 -22.512 0.467 23.296 119.808
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 248.14 39.58 6.269 1.50e-08 ***
bx1 -191.65 55.98 -3.424 0.000957 ***
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 117.89 5359.50 0.022 0.982503
bx5 -186.78 232.03 -0.805 0.423121
bx6 -100.88 59.89 -1.684 0.095837 .
bx7 115.65 45.41 2.547 0.012692 *
bx8 167.83 45.88 3.658 0.000443 ***
bx9 278.71 57.63 4.836 5.93e-06 ***
bx10 33.55 168.13 0.200 0.842302
bx11 -656.08 912.27 -0.719 0.474031
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 39.58 on 84 degrees of freedom
Multiple R-squared: 0.8246, Adjusted R-squared: 0.8058
F-statistic: 43.88 on 9 and 84 DF, p-value: < 2.2e-16
[1] "WT_L.1"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-140.112 -29.759 0.866 29.544 166.493
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 307.25 53.15 5.781 1.23e-07 ***
bx1 -230.86 75.16 -3.071 0.00287 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 682.20 7196.52 0.095 0.92470
bx5 -246.93 311.56 -0.793 0.43027
bx6 -108.69 80.42 -1.351 0.18017
bx7 201.63 60.97 3.307 0.00139 **
bx8 275.82 61.60 4.477 2.36e-05 ***
bx9 427.88 77.39 5.529 3.56e-07 ***
bx10 -8.42 225.76 -0.037 0.97034
bx11 -644.31 1224.95 -0.526 0.60028
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 53.15 on 84 degrees of freedom
Multiple R-squared: 0.84, Adjusted R-squared: 0.8229
F-statistic: 49.01 on 9 and 84 DF, p-value: < 2.2e-16
[1] "WT_L.2"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-152.192 -34.645 0.582 33.715 184.830
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 311.44 57.91 5.378 6.67e-07 ***
bx1 -234.46 81.90 -2.863 0.00530 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 1434.15 7841.71 0.183 0.85533
bx5 -283.46 339.50 -0.835 0.40613
bx6 -91.28 87.63 -1.042 0.30060
bx7 220.11 66.44 3.313 0.00136 **
bx8 300.89 67.13 4.482 2.32e-05 ***
bx9 462.58 84.33 5.486 4.26e-07 ***
bx10 24.31 246.00 0.099 0.92152
bx11 -712.80 1334.77 -0.534 0.59474
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 57.91 on 84 degrees of freedom
Multiple R-squared: 0.8293, Adjusted R-squared: 0.811
F-statistic: 45.34 on 9 and 84 DF, p-value: < 2.2e-16
[1] "GC content bias detection is to be computed for:"
[1] "WT_D" "WT_L"
[1] "WT_D"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-10.7083 -2.7214 -0.0951 2.4417 10.8768
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 29.210 4.197 6.960 6.96e-10 ***
bx1 -19.142 5.935 -3.225 0.001794 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 145.809 568.258 0.257 0.798123
bx5 -28.365 24.602 -1.153 0.252201
bx6 -5.836 6.351 -0.919 0.360732
bx7 17.412 4.814 3.617 0.000508 ***
bx8 21.788 4.864 4.479 2.35e-05 ***
bx9 9.421 6.111 1.542 0.126888
bx10 6.151 17.827 0.345 0.730923
bx11 -69.128 96.726 -0.715 0.476791
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 4.197 on 84 degrees of freedom
Multiple R-squared: 0.7803, Adjusted R-squared: 0.7568
F-statistic: 33.15 on 9 and 84 DF, p-value: < 2.2e-16
[1] "WT_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-13.0785 -2.8584 0.0593 2.8402 15.4467
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 28.851 4.964 5.812 1.08e-07 ***
bx1 -21.899 7.020 -3.119 0.00248 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 68.388 672.140 0.102 0.91920
bx5 -23.655 29.100 -0.813 0.41858
bx6 -10.202 7.511 -1.358 0.17804
bx7 17.398 5.695 3.055 0.00301 **
bx8 24.212 5.754 4.208 6.42e-05 ***
bx9 38.220 7.228 5.288 9.65e-07 ***
bx10 1.689 21.085 0.080 0.93636
bx11 -67.265 114.408 -0.588 0.55815
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 4.964 on 84 degrees of freedom
Multiple R-squared: 0.8315, Adjusted R-squared: 0.8134
F-statistic: 46.06 on 9 and 84 DF, p-value: < 2.2e-16
[1] "WT_D"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-10.7083 -2.7214 -0.0951 2.4417 10.8768
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 29.210 4.197 6.960 6.96e-10 ***
bx1 -19.142 5.935 -3.225 0.001794 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 145.809 568.258 0.257 0.798123
bx5 -28.365 24.602 -1.153 0.252201
bx6 -5.836 6.351 -0.919 0.360732
bx7 17.412 4.814 3.617 0.000508 ***
bx8 21.788 4.864 4.479 2.35e-05 ***
bx9 9.421 6.111 1.542 0.126888
bx10 6.151 17.827 0.345 0.730923
bx11 -69.128 96.726 -0.715 0.476791
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 4.197 on 84 degrees of freedom
Multiple R-squared: 0.7803, Adjusted R-squared: 0.7568
F-statistic: 33.15 on 9 and 84 DF, p-value: < 2.2e-16
[1] "WT_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-13.0785 -2.8584 0.0593 2.8402 15.4467
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 28.851 4.964 5.812 1.08e-07 ***
bx1 -21.899 7.020 -3.119 0.00248 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 68.388 672.140 0.102 0.91920
bx5 -23.655 29.100 -0.813 0.41858
bx6 -10.202 7.511 -1.358 0.17804
bx7 17.398 5.695 3.055 0.00301 **
bx8 24.212 5.754 4.208 6.42e-05 ***
bx9 38.220 7.228 5.288 9.65e-07 ***
bx10 1.689 21.085 0.080 0.93636
bx11 -67.265 114.408 -0.588 0.55815
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 4.964 on 84 degrees of freedom
Multiple R-squared: 0.8315, Adjusted R-squared: 0.8134
F-statistic: 46.06 on 9 and 84 DF, p-value: < 2.2e-16
[1] "Length bias detection information is to be computed for:"
[1] "WT_D" "WT_D.1" "WT_D.2" "WT_L" "WT_L.1" "WT_L.2"
[1] "WT_D"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-65.64 -22.32 -3.92 20.84 94.52
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 1107.46 33.61 32.952 < 2e-16 ***
bx1 -1069.25 46.87 -22.811 < 2e-16 ***
bx2 -979.16 48.85 -20.043 < 2e-16 ***
bx3 -804.82 42.17 -19.083 < 2e-16 ***
bx4 -868.48 38.07 -22.813 < 2e-16 ***
bx5 -737.20 38.11 -19.346 < 2e-16 ***
bx6 -723.17 40.31 -17.941 < 2e-16 ***
bx7 -591.10 45.87 -12.885 < 2e-16 ***
bx8 -600.16 62.02 -9.677 3.26e-15 ***
bx9 -322.94 129.42 -2.495 0.0146 *
bx10 -1506.94 1674.13 -0.900 0.3707
bx11 24871.69 27232.95 0.913 0.3638
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 33.61 on 82 degrees of freedom
Multiple R-squared: 0.9499, Adjusted R-squared: 0.9432
F-statistic: 141.4 on 11 and 82 DF, p-value: < 2.2e-16
[1] "WT_D.1"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-74.626 -24.660 -4.119 24.717 109.826
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 1170.83 37.40 31.308 < 2e-16 ***
bx1 -1126.97 52.16 -21.607 < 2e-16 ***
bx2 -1024.80 54.36 -18.852 < 2e-16 ***
bx3 -825.91 46.93 -17.599 < 2e-16 ***
bx4 -905.97 42.36 -21.387 < 2e-16 ***
bx5 -765.90 42.40 -18.063 < 2e-16 ***
bx6 -750.21 44.85 -16.726 < 2e-16 ***
bx7 -613.25 51.05 -12.014 < 2e-16 ***
bx8 -622.11 69.01 -9.014 6.74e-14 ***
bx9 -332.03 144.01 -2.306 0.0237 *
bx10 -1473.34 1862.87 -0.791 0.4313
bx11 24550.80 30303.02 0.810 0.4202
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 37.4 on 82 degrees of freedom
Multiple R-squared: 0.9439, Adjusted R-squared: 0.9363
F-statistic: 125.3 on 11 and 82 DF, p-value: < 2.2e-16
[1] "WT_D.2"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-85.583 -30.647 -4.321 29.139 134.932
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 1347.87 44.59 30.229 < 2e-16 ***
bx1 -1300.01 62.19 -20.905 < 2e-16 ***
bx2 -1185.21 64.81 -18.286 < 2e-16 ***
bx3 -926.06 55.95 -16.551 < 2e-16 ***
bx4 -1028.92 50.51 -20.372 < 2e-16 ***
bx5 -856.19 50.56 -16.936 < 2e-16 ***
bx6 -843.46 53.48 -15.772 < 2e-16 ***
bx7 -687.65 60.86 -11.299 < 2e-16 ***
bx8 -690.07 82.28 -8.386 1.2e-12 ***
bx9 -388.63 171.70 -2.263 0.0263 *
bx10 -1337.68 2221.06 -0.602 0.5487
bx11 22256.97 36129.71 0.616 0.5396
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 44.59 on 82 degrees of freedom
Multiple R-squared: 0.9404, Adjusted R-squared: 0.9324
F-statistic: 117.6 on 11 and 82 DF, p-value: < 2.2e-16
[1] "WT_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-70.167 -24.061 -0.371 19.335 109.589
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 690.83 39.80 17.356 < 2e-16 ***
bx1 -665.42 55.51 -11.987 < 2e-16 ***
bx2 -549.68 57.86 -9.500 7.28e-15 ***
bx3 -256.37 49.95 -5.133 1.89e-06 ***
bx4 -398.20 45.09 -8.832 1.55e-13 ***
bx5 -310.16 45.13 -6.873 1.13e-09 ***
bx6 -380.27 47.74 -7.966 8.17e-12 ***
bx7 -258.11 54.33 -4.751 8.51e-06 ***
bx8 -341.80 73.45 -4.653 1.24e-05 ***
bx9 -44.89 153.28 -0.293 0.770
bx10 -2277.69 1982.71 -1.149 0.254
bx11 36847.56 32252.56 1.142 0.257
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 39.8 on 82 degrees of freedom
Multiple R-squared: 0.7592, Adjusted R-squared: 0.7269
F-statistic: 23.5 on 11 and 82 DF, p-value: < 2.2e-16
[1] "WT_L.1"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-86.551 -32.542 -1.822 28.758 137.726
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 1008.97 52.21 19.324 < 2e-16 ***
bx1 -975.55 72.82 -13.396 < 2e-16 ***
bx2 -840.90 75.90 -11.079 < 2e-16 ***
bx3 -449.19 65.52 -6.855 1.22e-09 ***
bx4 -598.67 59.14 -10.122 4.28e-16 ***
bx5 -473.28 59.20 -7.994 7.17e-12 ***
bx6 -560.60 62.62 -8.952 8.97e-14 ***
bx7 -392.00 71.27 -5.500 4.21e-07 ***
bx8 -495.54 96.36 -5.143 1.81e-06 ***
bx9 -81.24 201.07 -0.404 0.687
bx10 -3062.59 2600.95 -1.177 0.242
bx11 48688.87 42309.34 1.151 0.253
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 52.21 on 82 degrees of freedom
Multiple R-squared: 0.8141, Adjusted R-squared: 0.7891
F-statistic: 32.64 on 11 and 82 DF, p-value: < 2.2e-16
[1] "WT_L.2"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-98.618 -35.585 -2.349 28.667 150.194
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 991.40 56.18 17.648 < 2e-16 ***
bx1 -959.13 78.35 -12.242 < 2e-16 ***
bx2 -808.12 81.66 -9.896 1.20e-15 ***
bx3 -378.43 70.50 -5.368 7.25e-07 ***
bx4 -555.64 63.63 -8.732 2.46e-13 ***
bx5 -430.80 63.70 -6.763 1.84e-09 ***
bx6 -529.18 67.38 -7.854 1.36e-11 ***
bx7 -360.58 76.68 -4.703 1.03e-05 ***
bx8 -468.43 103.67 -4.519 2.07e-05 ***
bx9 -44.06 216.33 -0.204 0.839
bx10 -3290.21 2798.33 -1.176 0.243
bx11 53052.09 45520.11 1.165 0.247
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 56.18 on 82 degrees of freedom
Multiple R-squared: 0.778, Adjusted R-squared: 0.7482
F-statistic: 26.13 on 11 and 82 DF, p-value: < 2.2e-16
[1] "Length bias detection information is to be computed for:"
[1] "WT_D" "WT_L"
[1] "WT_D"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-8.1313 -2.8273 -0.4555 2.6653 12.1392
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 130.755 4.146 31.541 < 2e-16 ***
bx1 -126.074 5.782 -21.806 < 2e-16 ***
bx2 -115.014 6.026 -19.086 < 2e-16 ***
bx3 -92.426 5.202 -17.767 < 2e-16 ***
bx4 -101.201 4.696 -21.552 < 2e-16 ***
bx5 -85.259 4.700 -18.139 < 2e-16 ***
bx6 -83.705 4.972 -16.836 < 2e-16 ***
bx7 -68.371 5.658 -12.083 < 2e-16 ***
bx8 -69.141 7.650 -9.038 6.05e-14 ***
bx9 -37.500 15.964 -2.349 0.0212 *
bx10 -158.200 206.500 -0.766 0.4458
bx11 2618.719 3359.109 0.780 0.4379
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 4.146 on 82 degrees of freedom
Multiple R-squared: 0.9451, Adjusted R-squared: 0.9377
F-statistic: 128.3 on 11 and 82 DF, p-value: < 2.2e-16
[1] "WT_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-8.4703 -2.9574 -0.1528 2.5954 13.1448
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 88.582 4.892 18.106 < 2e-16 ***
bx1 -85.552 6.823 -12.538 < 2e-16 ***
bx2 -72.195 7.112 -10.152 3.75e-16 ***
bx3 -35.429 6.139 -5.771 1.36e-07 ***
bx4 -51.125 5.542 -9.225 2.56e-14 ***
bx5 -39.930 5.547 -7.198 2.64e-10 ***
bx6 -48.443 5.868 -8.256 2.17e-12 ***
bx7 -33.253 6.678 -4.980 3.47e-06 ***
bx8 -43.094 9.029 -4.773 7.81e-06 ***
bx9 -5.447 18.840 -0.289 0.773
bx10 -287.290 243.705 -1.179 0.242
bx11 4618.402 3964.314 1.165 0.247
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 4.892 on 82 degrees of freedom
Multiple R-squared: 0.7845, Adjusted R-squared: 0.7556
F-statistic: 27.14 on 11 and 82 DF, p-value: < 2.2e-16
[1] "WT_D"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-8.1313 -2.8273 -0.4555 2.6653 12.1392
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 130.755 4.146 31.541 < 2e-16 ***
bx1 -126.074 5.782 -21.806 < 2e-16 ***
bx2 -115.014 6.026 -19.086 < 2e-16 ***
bx3 -92.426 5.202 -17.767 < 2e-16 ***
bx4 -101.201 4.696 -21.552 < 2e-16 ***
bx5 -85.259 4.700 -18.139 < 2e-16 ***
bx6 -83.705 4.972 -16.836 < 2e-16 ***
bx7 -68.371 5.658 -12.083 < 2e-16 ***
bx8 -69.141 7.650 -9.038 6.05e-14 ***
bx9 -37.500 15.964 -2.349 0.0212 *
bx10 -158.200 206.500 -0.766 0.4458
bx11 2618.719 3359.109 0.780 0.4379
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 4.146 on 82 degrees of freedom
Multiple R-squared: 0.9451, Adjusted R-squared: 0.9377
F-statistic: 128.3 on 11 and 82 DF, p-value: < 2.2e-16
[1] "WT_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-8.4703 -2.9574 -0.1528 2.5954 13.1448
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 88.582 4.892 18.106 < 2e-16 ***
bx1 -85.552 6.823 -12.538 < 2e-16 ***
bx2 -72.195 7.112 -10.152 3.75e-16 ***
bx3 -35.429 6.139 -5.771 1.36e-07 ***
bx4 -51.125 5.542 -9.225 2.56e-14 ***
bx5 -39.930 5.547 -7.198 2.64e-10 ***
bx6 -48.443 5.868 -8.256 2.17e-12 ***
bx7 -33.253 6.678 -4.980 3.47e-06 ***
bx8 -43.094 9.029 -4.773 7.81e-06 ***
bx9 -5.447 18.840 -0.289 0.773
bx10 -287.290 243.705 -1.179 0.242
bx11 4618.402 3964.314 1.165 0.247
bx12 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 4.892 on 82 degrees of freedom
Multiple R-squared: 0.7845, Adjusted R-squared: 0.7556
F-statistic: 27.14 on 11 and 82 DF, p-value: < 2.2e-16
[1] "Reference sample is: WT_D"
[1] "Confidence intervals for median of M:"
0.5% 99.5% Diagnostic Test
WT_D.1 "-0.0128515513393805" "-0.00444112472539529" "FAILED"
WT_D.2 "0.0201324209522599" "0.0294615081891506" "FAILED"
WT_L "-0.0323911690247728" "0.0210496097254537" "PASSED"
WT_L.1 "-0.0164339490427685" "0.0397848555427504" "PASSED"
WT_L.2 "-0.0224583638134474" "0.0344243649120653" "PASSED"
[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...
18198 features are to be kept for differential expression analysis with filtering method 1
...k-means clustering done
Size of 15 clusters:
[1] 5143 160 63 14 976 1203 34 228 4 406 29 217 9634 19 68
Resampling cluster...[1] 1
Size of 15 subclusters of cluster: 1
[1] 505 496 388 183 394 214 335 239 615 220 547 308 182 219 298
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
Size of 15 subclusters of cluster: 6
[1] 105 73 86 55 77 50 99 93 67 52 144 44 61 62 135
[1] 7
[1] 8
[1] 9
[1] 10
[1] 11
[1] 12
[1] 13
Size of 15 subclusters of cluster: 13
[1] 651 791 543 615 567 410 527 275 236 425 953 382 1502 787 970
[1] 14
[1] 15
Computing Z for noise...
Computing probability of differential expression...
p0 = 0.0905990870170189
Probability
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.9361 0.9948 0.9059 0.9999 1.0000 623
Computing Z values...
Filtering out low count features...
18821 features are to be kept for differential expression analysis with filtering method 1
...k-means clustering done
Size of 15 clusters:
[1] 14 4 19 407 29 63 5341 217 984 10025 160 1228 228 68 34
Resampling cluster...[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
Size of 15 subclusters of cluster: 7
[1] 297 397 347 563 524 670 391 537 356 229 221 228 181 182 218
[1] 8
[1] 9
[1] 10
Size of 15 subclusters of cluster: 10
[1] 967 620 820 546 524 235 422 264 585 632 947 774 1930 400 359
[1] 11
[1] 12
Size of 15 subclusters of cluster: 12
[1] 57 97 100 50 117 61 80 41 63 89 152 49 64 164 44
[1] 13
[1] 14
[1] 15
Computing Z for noise...
Computing probability of differential expression...
p0 = 0.0953473287565793
Probability
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.0000 0.9324 0.9940 0.9010 0.9999 1.0000
Computing Z values...
Filtering out low count features...
18821 features are to be kept for differential expression analysis with filtering method 1
...k-means clustering done
Size of 15 clusters:
[1] 387 239 67 298 15 96 2412 102 995 5207 1278 36 4 36 7649
Resampling cluster...[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
Size of 15 subclusters of cluster: 7
[1] 163 239 232 109 116 171 197 187 130 146 93 145 282 64 138
[1] 8
[1] 9
[1] 10
Size of 15 subclusters of cluster: 10
[1] 188 326 515 182 296 446 341 648 396 383 272 228 349 233 404
[1] 11
Size of 15 subclusters of cluster: 11
[1] 65 97 127 142 53 99 112 55 77 107 61 71 104 48 60
[1] 12
[1] 13
[1] 14
[1] 15
Size of 15 subclusters of cluster: 15
[1] 302 719 459 305 640 402 1885 477 527 240 403 181 136 648 325
Computing Z for noise...
Computing probability of differential expression...
p0 = 0.151229384998821
Probability
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.0000 0.8249 0.9726 0.8433 0.9987 1.0000
[1] "8967 differentially expressed features"
[1] "4119 differentially expressed features (up in first condition)"
[1] "4848 differentially expressed features (down in first condition)"
[1] "6502 differentially expressed features"
[1] "2473 differentially expressed features (up in first condition)"
[1] "4029 differentially expressed features (down in first condition)"
[1] "7773 differentially expressed features"
[1] "10808 differentially expressed features"
[1] "4189 differentially expressed features"
[1] "6177 differentially expressed features"
[1] "7801 differentially expressed features"
[1] "10814 differentially expressed features"
[1] "14528 differentially expressed features"
[1] "8967 differentially expressed features"
[1] "12619 differentially expressed features"
[1] "6502 differentially expressed features"
[1] "7773 differentially expressed features"
[1] "4189 differentially expressed features"
[1] "DEGs edgeR"
[1] 13555
[1] "DEGs deseq2"
[1] 11922
[1] "DEGs noiseq"
[1] 7773
[1] "DEGs noiseqbio"
[1] 8967
[1] "DEGs intersection without direction check (four methods)"
[1] 7377
[1] "Pp3c1_40V3.1" "Pp3c1_200V3.1" "Pp3c1_370V3.1" "Pp3c1_470V3.1" "Pp3c1_540V3.1" "Pp3c1_580V3.1" "Pp3c1_680V3.1"
[8] "Pp3c1_690V3.1" "Pp3c1_890V3.1" "Pp3c1_900V3.1" "Pp3c1_950V3.1" "Pp3c1_1000V3.1" "Pp3c1_1160V3.1" "Pp3c1_1260V3.1"
[15] "Pp3c1_1330V3.1" "Pp3c1_1360V3.1" "Pp3c1_1390V3.1" "Pp3c1_1570V3.1" "Pp3c1_1800V3.1" "Pp3c1_1810V3.1" "Pp3c1_1860V3.1"
[22] "Pp3c1_1870V3.1" "Pp3c1_1940V3.1" "Pp3c1_2170V3.1" "Pp3c1_2210V3.1" "Pp3c1_2220V3.1" "Pp3c1_2420V3.1" "Pp3c1_2540V3.1"
[29] "Pp3c1_2740V3.1" "Pp3c1_2920V3.1" "Pp3c1_2980V3.1" "Pp3c1_3040V3.1" "Pp3c1_3160V3.1" "Pp3c1_3180V3.1" "Pp3c1_3200V3.1"
[36] "Pp3c1_3210V3.1" "Pp3c1_3220V3.1" "Pp3c1_3300V3.1" "Pp3c1_3500V3.1" "Pp3c1_3590V3.1" "Pp3c1_3610V3.1" "Pp3c1_3700V3.1"
[43] "Pp3c1_3730V3.1" "Pp3c1_3750V3.1" "Pp3c1_3890V3.1" "Pp3c1_4010V3.1" "Pp3c1_4030V3.1" "Pp3c1_4050V3.1" "Pp3c1_4140V3.1"
[50] "Pp3c1_4180V3.1" "Pp3c1_4270V3.1" "Pp3c1_4300V3.1" "Pp3c1_4350V3.1" "Pp3c1_4470V3.1" "Pp3c1_4600V3.1" "Pp3c1_4750V3.1"
[57] "Pp3c1_4990V3.1" "Pp3c1_5050V3.1" "Pp3c1_5280V3.1" "Pp3c1_5300V3.1" "Pp3c1_5320V3.1" "Pp3c1_5460V3.1" "Pp3c1_5570V3.1"
[64] "Pp3c1_5800V3.1" "Pp3c1_5820V3.1" "Pp3c1_5850V3.1" "Pp3c1_6020V3.1" "Pp3c1_6050V3.1" "Pp3c1_6090V3.1" "Pp3c1_6110V3.1"
[71] "Pp3c1_6272V3.1" "Pp3c1_6280V3.1" "Pp3c1_6360V3.1" "Pp3c1_6450V3.1" "Pp3c1_6470V3.1" "Pp3c1_6480V3.1" "Pp3c1_6500V3.1"
[78] "Pp3c1_6570V3.1" "Pp3c1_6640V3.1" "Pp3c1_6750V3.1" "Pp3c1_6930V3.1" "Pp3c1_6980V3.1" "Pp3c1_7030V3.1" "Pp3c1_7160V3.1"
[85] "Pp3c1_7170V3.1" "Pp3c1_7300V3.1" "Pp3c1_7370V3.1" "Pp3c1_7380V3.1" "Pp3c1_7450V3.1" "Pp3c1_7500V3.1" "Pp3c1_7520V3.1"
[92] "Pp3c1_7540V3.1" "Pp3c1_7590V3.1" "Pp3c1_7710V3.1" "Pp3c1_7720V3.1" "Pp3c1_7810V3.1" "Pp3c1_7830V3.1" "Pp3c1_7880V3.1"
[99] "Pp3c1_7910V3.1" "Pp3c1_7950V3.1" "Pp3c1_8060V3.1" "Pp3c1_8080V3.1" "Pp3c1_8110V3.1" "Pp3c1_8170V3.1" "Pp3c1_8190V3.1"
[106] "Pp3c1_8280V3.1" "Pp3c1_8440V3.1" "Pp3c1_8530V3.1" "Pp3c1_8550V3.1" "Pp3c1_8870V3.1" "Pp3c1_8890V3.1" "Pp3c1_9180V3.1"
[113] "Pp3c1_9250V3.1" "Pp3c1_9290V3.1" "Pp3c1_9320V3.1" "Pp3c1_9560V3.1" "Pp3c1_9600V3.1" "Pp3c1_9630V3.1" "Pp3c1_9790V3.1"
[120] "Pp3c1_9860V3.1" "Pp3c1_9970V3.1" "Pp3c1_10010V3.1" "Pp3c1_10080V3.1" "Pp3c1_10090V3.1" "Pp3c1_10100V3.1" "Pp3c1_10180V3.1"
[127] "Pp3c1_10220V3.1" "Pp3c1_10400V3.1" "Pp3c1_10470V3.1" "Pp3c1_10540V3.1" "Pp3c1_10570V3.1" "Pp3c1_10620V3.1" "Pp3c1_10810V3.1"
[134] "Pp3c1_10880V3.1" "Pp3c1_10970V3.1" "Pp3c1_11030V3.1" "Pp3c1_11050V3.1" "Pp3c1_11090V3.1" "Pp3c1_11190V3.1" "Pp3c1_11980V3.1"
[141] "Pp3c1_12020V3.1" "Pp3c1_12100V3.1" "Pp3c1_12120V3.1" "Pp3c1_12140V3.1" "Pp3c1_12470V3.1" "Pp3c1_12610V3.1" "Pp3c1_12630V3.1"
[148] "Pp3c1_12730V3.1" "Pp3c1_12790V3.1" "Pp3c1_12810V3.1" "Pp3c1_12850V3.1" "Pp3c1_12860V3.1" "Pp3c1_12940V3.1" "Pp3c1_13120V3.1"
[155] "Pp3c1_13170V3.1" "Pp3c1_13308V3.1" "Pp3c1_13430V3.1" "Pp3c1_13570V3.1" "Pp3c1_13640V3.1" "Pp3c1_13670V3.1" "Pp3c1_13671V3.1"
[162] "Pp3c1_13830V3.1" "Pp3c1_13910V3.1" "Pp3c1_14230V3.1" "Pp3c1_14330V3.1" "Pp3c1_14380V3.1" "Pp3c1_14670V3.1" "Pp3c1_14740V3.1"
[169] "Pp3c1_14760V3.1" "Pp3c1_14770V3.1" "Pp3c1_14800V3.1" "Pp3c1_14870V3.1" "Pp3c1_14910V3.1" "Pp3c1_14980V3.1" "Pp3c1_15010V3.1"
[176] "Pp3c1_15100V3.1" "Pp3c1_15110V3.1" "Pp3c1_15150V3.1" "Pp3c1_15160V3.1" "Pp3c1_15210V3.1" "Pp3c1_15400V3.1" "Pp3c1_15410V3.1"
[183] "Pp3c1_15490V3.1" "Pp3c1_15560V3.1" "Pp3c1_15690V3.1" "Pp3c1_15730V3.1" "Pp3c1_15750V3.1" "Pp3c1_15940V3.1" "Pp3c1_16170V3.1"
[190] "Pp3c1_16250V3.1" "Pp3c1_16260V3.1" "Pp3c1_16500V3.1" "Pp3c1_16600V3.1" "Pp3c1_16780V3.1" "Pp3c1_16840V3.1" "Pp3c1_16850V3.1"
[197] "Pp3c1_16900V3.1" "Pp3c1_16980V3.1" "Pp3c1_17080V3.1" "Pp3c1_17220V3.1" "Pp3c1_17370V3.1" "Pp3c1_17870V3.1" "Pp3c1_18130V3.1"
[204] "Pp3c1_18260V3.1" "Pp3c1_18420V3.1" "Pp3c1_18440V3.1" "Pp3c1_18460V3.1" "Pp3c1_18530V3.1" "Pp3c1_18830V3.1" "Pp3c1_18860V3.1"
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[736] "Pp3c2_17540V3.1" "Pp3c2_17560V3.1" "Pp3c2_17640V3.1" "Pp3c2_17670V3.1" "Pp3c2_17700V3.1" "Pp3c2_17710V3.1" "Pp3c2_17900V3.1"
[743] "Pp3c2_17910V3.1" "Pp3c2_18020V3.1" "Pp3c2_18110V3.1" "Pp3c2_18130V3.1" "Pp3c2_18330V3.1" "Pp3c2_18450V3.1" "Pp3c2_18480V3.1"
[750] "Pp3c2_18510V3.1" "Pp3c2_18520V3.1" "Pp3c2_18540V3.1" "Pp3c2_18600V3.1" "Pp3c2_18850V3.1" "Pp3c2_19150V3.1" "Pp3c2_19170V3.1"
[757] "Pp3c2_19250V3.1" "Pp3c2_19260V3.1" "Pp3c2_19310V3.1" "Pp3c2_19330V3.1" "Pp3c2_19380V3.1" "Pp3c2_19400V3.1" "Pp3c2_19430V3.1"
[764] "Pp3c2_19520V3.1" "Pp3c2_19550V3.1" "Pp3c2_19610V3.1" "Pp3c2_19700V3.1" "Pp3c2_19940V3.1" "Pp3c2_19980V3.1" "Pp3c2_20030V3.1"
[771] "Pp3c2_20130V3.1" "Pp3c2_20141V3.1" "Pp3c2_20320V3.1" "Pp3c2_20330V3.1" "Pp3c2_20450V3.1" "Pp3c2_20500V3.1" "Pp3c2_20550V3.1"
[778] "Pp3c2_20630V3.1" "Pp3c2_20660V3.1" "Pp3c2_20840V3.1" "Pp3c2_20860V3.1" "Pp3c2_20930V3.1" "Pp3c2_21110V3.1" "Pp3c2_21270V3.1"
[785] "Pp3c2_21290V3.1" "Pp3c2_21310V3.1" "Pp3c2_21370V3.1" "Pp3c2_21470V3.1" "Pp3c2_21580V3.1" "Pp3c2_21590V3.1" "Pp3c2_21600V3.1"
[792] "Pp3c2_21710V3.1" "Pp3c2_21860V3.1" "Pp3c2_21970V3.1" "Pp3c2_22000V3.1" "Pp3c2_22020V3.1" "Pp3c2_22140V3.1" "Pp3c2_22190V3.1"
[799] "Pp3c2_22310V3.1" "Pp3c2_22630V3.1" "Pp3c2_23100V3.1" "Pp3c2_23140V3.1" "Pp3c2_23200V3.1" "Pp3c2_23290V3.1" "Pp3c2_23300V3.1"
[806] "Pp3c2_23590V3.1" "Pp3c2_23870V3.1" "Pp3c2_23900V3.1" "Pp3c2_24130V3.1" "Pp3c2_24150V3.1" "Pp3c2_24160V3.1" "Pp3c2_24270V3.1"
[813] "Pp3c2_24620V3.1" "Pp3c2_24640V3.1" "Pp3c2_24723V3.1" "Pp3c2_24761V3.1" "Pp3c2_24840V3.1" "Pp3c2_24870V3.1" "Pp3c2_25000V3.1"
[820] "Pp3c2_25160V3.1" "Pp3c2_25170V3.1" "Pp3c2_25580V3.1" "Pp3c2_25620V3.1" "Pp3c2_25690V3.1" "Pp3c2_25720V3.1" "Pp3c2_25890V3.1"
[827] "Pp3c2_25930V3.1" "Pp3c2_26060V3.1" "Pp3c2_26200V3.1" "Pp3c2_26250V3.1" "Pp3c2_26270V3.1" "Pp3c2_26320V3.1" "Pp3c2_26540V3.1"
[834] "Pp3c2_26550V3.1" "Pp3c2_26650V3.1" "Pp3c2_26700V3.1" "Pp3c2_26720V3.1" "Pp3c2_26970V3.1" "Pp3c2_27180V3.1" "Pp3c2_27330V3.1"
[841] "Pp3c2_27340V3.1" "Pp3c2_27350V3.1" "Pp3c2_27440V3.1" "Pp3c2_27480V3.1" "Pp3c2_27510V3.1" "Pp3c2_27540V3.1" "Pp3c2_27550V3.1"
[848] "Pp3c2_27590V3.1" "Pp3c2_27820V3.1" "Pp3c2_27910V3.1" "Pp3c2_27940V3.1" "Pp3c2_27970V3.1" "Pp3c2_27980V3.1" "Pp3c2_28030V3.1"
[855] "Pp3c2_28040V3.1" "Pp3c2_28130V3.1" "Pp3c2_28140V3.1" "Pp3c2_28162V3.1" "Pp3c2_28180V3.1" "Pp3c2_28380V3.1" "Pp3c2_28420V3.1"
[862] "Pp3c2_28540V3.1" "Pp3c2_28550V3.1" "Pp3c2_28570V3.1" "Pp3c2_28690V3.1" "Pp3c2_28870V3.1" "Pp3c2_29040V3.1" "Pp3c2_29249V3.1"
[869] "Pp3c2_29290V3.1" "Pp3c2_29500V3.1" "Pp3c2_29800V3.1" "Pp3c2_29840V3.1" "Pp3c2_30030V3.1" "Pp3c2_30040V3.1" "Pp3c2_30060V3.1"
[876] "Pp3c2_30250V3.1" "Pp3c2_30340V3.1" "Pp3c2_30370V3.1" "Pp3c2_30390V3.1" "Pp3c2_30510V3.1" "Pp3c2_30530V3.1" "Pp3c2_30580V3.1"
[883] "Pp3c2_30600V3.1" "Pp3c2_30610V3.1" "Pp3c2_30620V3.1" "Pp3c2_30630V3.1" "Pp3c2_30720V3.1" "Pp3c2_30770V3.1" "Pp3c2_30860V3.1"
[890] "Pp3c2_30940V3.1" "Pp3c2_30970V3.1" "Pp3c2_30980V3.1" "Pp3c2_31241V3.1" "Pp3c2_31270V3.1" "Pp3c2_31280V3.1" "Pp3c2_31330V3.1"
[897] "Pp3c2_31470V3.1" "Pp3c2_31540V3.1" "Pp3c2_31580V3.1" "Pp3c2_31590V3.1" "Pp3c2_31610V3.1" "Pp3c2_31930V3.1" "Pp3c2_32270V3.1"
[904] "Pp3c2_32310V3.1" "Pp3c2_32320V3.1" "Pp3c2_32400V3.1" "Pp3c2_32540V3.1" "Pp3c2_32600V3.1" "Pp3c2_32610V3.1" "Pp3c2_32690V3.1"
[911] "Pp3c2_32740V3.1" "Pp3c2_32770V3.1" "Pp3c2_32860V3.1" "Pp3c2_32990V3.1" "Pp3c2_33330V3.1" "Pp3c2_33430V3.1" "Pp3c2_33800V3.1"
[918] "Pp3c2_33890V3.1" "Pp3c2_33980V3.1" "Pp3c2_34110V3.1" "Pp3c2_34120V3.1" "Pp3c2_34130V3.1" "Pp3c2_34270V3.1" "Pp3c2_34310V3.1"
[925] "Pp3c2_34540V3.1" "Pp3c2_34550V3.1" "Pp3c2_34630V3.1" "Pp3c2_34670V3.1" "Pp3c2_34780V3.1" "Pp3c2_34820V3.1" "Pp3c2_34830V3.1"
[932] "Pp3c2_34890V3.1" "Pp3c2_34930V3.1" "Pp3c2_35010V3.1" "Pp3c2_35170V3.1" "Pp3c2_35200V3.1" "Pp3c2_35250V3.1" "Pp3c2_35530V3.1"
[939] "Pp3c2_35700V3.1" "Pp3c2_35740V3.1" "Pp3c2_35800V3.1" "Pp3c2_35870V3.1" "Pp3c2_35910V3.1" "Pp3c2_35930V3.1" "Pp3c2_35940V3.1"
[946] "Pp3c2_35950V3.1" "Pp3c2_36100V3.1" "Pp3c2_36220V3.1" "Pp3c2_36460V3.1" "Pp3c2_36480V3.1" "Pp3c2_36570V3.1" "Pp3c2_36790V3.1"
[953] "Pp3c2_36860V3.1" "Pp3c2_36990V3.1" "Pp3c2_37190V3.1" "Pp3c2_37210V3.1" "Pp3c2_37290V3.1" "Pp3c2_37299V3.1" "Pp3c2_37310V3.1"
[960] "Pp3c2_37670V3.1" "Pp3c2_37790V3.1" "Pp3c2_37900V3.1" "Pp3c2_37920V3.1" "Pp3c2_37990V3.1" "Pp3c2_38020V3.1" "Pp3c2_38120V3.1"
[967] "Pp3c2_38140V3.1" "Pp3c2_38160V3.1" "Pp3c2_38210V3.1" "Pp3c3_240V3.1" "Pp3c3_330V3.1" "Pp3c3_340V3.1" "Pp3c3_430V3.1"
[974] "Pp3c3_490V3.1" "Pp3c3_690V3.1" "Pp3c3_810V3.1" "Pp3c3_884V3.1" "Pp3c3_950V3.1" "Pp3c3_1020V3.1" "Pp3c3_1090V3.1"
[981] "Pp3c3_1160V3.1" "Pp3c3_1164V3.1" "Pp3c3_1500V3.1" "Pp3c3_1630V3.1" "Pp3c3_1700V3.1" "Pp3c3_1740V3.1" "Pp3c3_1750V3.1"
[988] "Pp3c3_1820V3.1" "Pp3c3_1910V3.1" "Pp3c3_2100V3.1" "Pp3c3_2130V3.1" "Pp3c3_2140V3.1" "Pp3c3_2240V3.1" "Pp3c3_2290V3.1"
[995] "Pp3c3_2380V3.1" "Pp3c3_2450V3.1" "Pp3c3_2620V3.1" "Pp3c3_2690V3.1" "Pp3c3_2730V3.1" "Pp3c3_2740V3.1"
[ reached getOption("max.print") -- omitted 6377 entries ]
[1] "DEGs intersection with direction check"
[1] 7377
[1] "Pp3c1_40V3.1" "Pp3c1_200V3.1" "Pp3c1_370V3.1" "Pp3c1_470V3.1" "Pp3c1_540V3.1" "Pp3c1_580V3.1" "Pp3c1_680V3.1"
[8] "Pp3c1_690V3.1" "Pp3c1_890V3.1" "Pp3c1_900V3.1" "Pp3c1_950V3.1" "Pp3c1_1000V3.1" "Pp3c1_1160V3.1" "Pp3c1_1260V3.1"
[15] "Pp3c1_1330V3.1" "Pp3c1_1360V3.1" "Pp3c1_1390V3.1" "Pp3c1_1570V3.1" "Pp3c1_1800V3.1" "Pp3c1_1810V3.1" "Pp3c1_1860V3.1"
[22] "Pp3c1_1870V3.1" "Pp3c1_1940V3.1" "Pp3c1_2170V3.1" "Pp3c1_2210V3.1" "Pp3c1_2220V3.1" "Pp3c1_2420V3.1" "Pp3c1_2540V3.1"
[29] "Pp3c1_2740V3.1" "Pp3c1_2920V3.1" "Pp3c1_2980V3.1" "Pp3c1_3040V3.1" "Pp3c1_3160V3.1" "Pp3c1_3180V3.1" "Pp3c1_3200V3.1"
[36] "Pp3c1_3210V3.1" "Pp3c1_3220V3.1" "Pp3c1_3300V3.1" "Pp3c1_3500V3.1" "Pp3c1_3590V3.1" "Pp3c1_3610V3.1" "Pp3c1_3700V3.1"
[43] "Pp3c1_3730V3.1" "Pp3c1_3750V3.1" "Pp3c1_3890V3.1" "Pp3c1_4010V3.1" "Pp3c1_4030V3.1" "Pp3c1_4050V3.1" "Pp3c1_4140V3.1"
[50] "Pp3c1_4180V3.1" "Pp3c1_4270V3.1" "Pp3c1_4300V3.1" "Pp3c1_4350V3.1" "Pp3c1_4470V3.1" "Pp3c1_4600V3.1" "Pp3c1_4750V3.1"
[57] "Pp3c1_4990V3.1" "Pp3c1_5050V3.1" "Pp3c1_5280V3.1" "Pp3c1_5300V3.1" "Pp3c1_5320V3.1" "Pp3c1_5460V3.1" "Pp3c1_5570V3.1"
[64] "Pp3c1_5800V3.1" "Pp3c1_5820V3.1" "Pp3c1_5850V3.1" "Pp3c1_6020V3.1" "Pp3c1_6050V3.1" "Pp3c1_6090V3.1" "Pp3c1_6110V3.1"
[71] "Pp3c1_6272V3.1" "Pp3c1_6280V3.1" "Pp3c1_6360V3.1" "Pp3c1_6450V3.1" "Pp3c1_6470V3.1" "Pp3c1_6480V3.1" "Pp3c1_6500V3.1"
[78] "Pp3c1_6570V3.1" "Pp3c1_6640V3.1" "Pp3c1_6750V3.1" "Pp3c1_6930V3.1" "Pp3c1_6980V3.1" "Pp3c1_7030V3.1" "Pp3c1_7160V3.1"
[85] "Pp3c1_7170V3.1" "Pp3c1_7300V3.1" "Pp3c1_7370V3.1" "Pp3c1_7380V3.1" "Pp3c1_7450V3.1" "Pp3c1_7500V3.1" "Pp3c1_7520V3.1"
[92] "Pp3c1_7540V3.1" "Pp3c1_7590V3.1" "Pp3c1_7710V3.1" "Pp3c1_7720V3.1" "Pp3c1_7810V3.1" "Pp3c1_7830V3.1" "Pp3c1_7880V3.1"
[99] "Pp3c1_7910V3.1" "Pp3c1_7950V3.1" "Pp3c1_8060V3.1" "Pp3c1_8080V3.1" "Pp3c1_8110V3.1" "Pp3c1_8170V3.1" "Pp3c1_8190V3.1"
[106] "Pp3c1_8280V3.1" "Pp3c1_8440V3.1" "Pp3c1_8530V3.1" "Pp3c1_8550V3.1" "Pp3c1_8870V3.1" "Pp3c1_8890V3.1" "Pp3c1_9180V3.1"
[113] "Pp3c1_9250V3.1" "Pp3c1_9290V3.1" "Pp3c1_9320V3.1" "Pp3c1_9560V3.1" "Pp3c1_9600V3.1" "Pp3c1_9630V3.1" "Pp3c1_9790V3.1"
[120] "Pp3c1_9860V3.1" "Pp3c1_9970V3.1" "Pp3c1_10010V3.1" "Pp3c1_10080V3.1" "Pp3c1_10090V3.1" "Pp3c1_10100V3.1" "Pp3c1_10180V3.1"
[127] "Pp3c1_10220V3.1" "Pp3c1_10400V3.1" "Pp3c1_10470V3.1" "Pp3c1_10540V3.1" "Pp3c1_10570V3.1" "Pp3c1_10620V3.1" "Pp3c1_10810V3.1"
[134] "Pp3c1_10880V3.1" "Pp3c1_10970V3.1" "Pp3c1_11030V3.1" "Pp3c1_11050V3.1" "Pp3c1_11090V3.1" "Pp3c1_11190V3.1" "Pp3c1_11980V3.1"
[141] "Pp3c1_12020V3.1" "Pp3c1_12100V3.1" "Pp3c1_12120V3.1" "Pp3c1_12140V3.1" "Pp3c1_12470V3.1" "Pp3c1_12610V3.1" "Pp3c1_12630V3.1"
[148] "Pp3c1_12730V3.1" "Pp3c1_12790V3.1" "Pp3c1_12810V3.1" "Pp3c1_12850V3.1" "Pp3c1_12860V3.1" "Pp3c1_12940V3.1" "Pp3c1_13120V3.1"
[155] "Pp3c1_13170V3.1" "Pp3c1_13308V3.1" "Pp3c1_13430V3.1" "Pp3c1_13570V3.1" "Pp3c1_13640V3.1" "Pp3c1_13670V3.1" "Pp3c1_13671V3.1"
[162] "Pp3c1_13830V3.1" "Pp3c1_13910V3.1" "Pp3c1_14230V3.1" "Pp3c1_14330V3.1" "Pp3c1_14380V3.1" "Pp3c1_14670V3.1" "Pp3c1_14740V3.1"
[169] "Pp3c1_14760V3.1" "Pp3c1_14770V3.1" "Pp3c1_14800V3.1" "Pp3c1_14870V3.1" "Pp3c1_14910V3.1" "Pp3c1_14980V3.1" "Pp3c1_15010V3.1"
[176] "Pp3c1_15100V3.1" "Pp3c1_15110V3.1" "Pp3c1_15150V3.1" "Pp3c1_15160V3.1" "Pp3c1_15210V3.1" "Pp3c1_15400V3.1" "Pp3c1_15410V3.1"
[183] "Pp3c1_15490V3.1" "Pp3c1_15560V3.1" "Pp3c1_15690V3.1" "Pp3c1_15730V3.1" "Pp3c1_15750V3.1" "Pp3c1_15940V3.1" "Pp3c1_16170V3.1"
[190] "Pp3c1_16250V3.1" "Pp3c1_16260V3.1" "Pp3c1_16500V3.1" "Pp3c1_16600V3.1" "Pp3c1_16780V3.1" "Pp3c1_16840V3.1" "Pp3c1_16850V3.1"
[197] "Pp3c1_16900V3.1" "Pp3c1_16980V3.1" "Pp3c1_17080V3.1" "Pp3c1_17220V3.1" "Pp3c1_17370V3.1" "Pp3c1_17870V3.1" "Pp3c1_18130V3.1"
[204] "Pp3c1_18260V3.1" "Pp3c1_18420V3.1" "Pp3c1_18440V3.1" "Pp3c1_18460V3.1" "Pp3c1_18530V3.1" "Pp3c1_18830V3.1" "Pp3c1_18860V3.1"
[211] "Pp3c1_18910V3.1" "Pp3c1_18940V3.1" "Pp3c1_19060V3.1" "Pp3c1_19176V3.1" "Pp3c1_19210V3.1" "Pp3c1_19230V3.1" "Pp3c1_19240V3.1"
[218] "Pp3c1_19370V3.1" "Pp3c1_19400V3.1" "Pp3c1_19590V3.1" "Pp3c1_20010V3.1" "Pp3c1_20040V3.1" "Pp3c1_20050V3.1" "Pp3c1_20280V3.1"
[225] "Pp3c1_20310V3.1" "Pp3c1_20610V3.1" "Pp3c1_20640V3.1" "Pp3c1_20690V3.1" "Pp3c1_20700V3.1" "Pp3c1_20753V3.1" "Pp3c1_20770V3.1"
[232] "Pp3c1_20870V3.1" "Pp3c1_20880V3.1" "Pp3c1_20960V3.1" "Pp3c1_20980V3.1" "Pp3c1_21050V3.1" "Pp3c1_21160V3.1" "Pp3c1_21200V3.1"
[239] "Pp3c1_21230V3.1" "Pp3c1_21270V3.1" "Pp3c1_21290V3.1" "Pp3c1_21360V3.1" "Pp3c1_21400V3.1" "Pp3c1_21480V3.1" "Pp3c1_21510V3.1"
[246] "Pp3c1_21540V3.1" "Pp3c1_21550V3.1" "Pp3c1_21650V3.1" "Pp3c1_21730V3.1" "Pp3c1_21760V3.1" "Pp3c1_21810V3.1" "Pp3c1_21890V3.1"
[253] "Pp3c1_21920V3.1" "Pp3c1_22090V3.1" "Pp3c1_22120V3.1" "Pp3c1_22260V3.1" "Pp3c1_22360V3.1" "Pp3c1_22450V3.1" "Pp3c1_22520V3.1"
[260] "Pp3c1_22540V3.1" "Pp3c1_22560V3.1" "Pp3c1_22590V3.1" "Pp3c1_22690V3.1" "Pp3c1_22710V3.1" "Pp3c1_22900V3.1" "Pp3c1_22950V3.1"
[267] "Pp3c1_23000V3.1" "Pp3c1_23010V3.1" "Pp3c1_23040V3.1" "Pp3c1_23190V3.1" "Pp3c1_23250V3.1" "Pp3c1_23260V3.1" "Pp3c1_23300V3.1"
[274] "Pp3c1_23410V3.1" "Pp3c1_23490V3.1" "Pp3c1_23520V3.1" "Pp3c1_23590V3.1" "Pp3c1_23600V3.1" "Pp3c1_23750V3.1" "Pp3c1_23850V3.1"
[281] "Pp3c1_23900V3.1" "Pp3c1_23920V3.1" "Pp3c1_23930V3.1" "Pp3c1_23960V3.1" "Pp3c1_23970V3.1" "Pp3c1_24000V3.1" "Pp3c1_24120V3.1"
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[813] "Pp3c2_24620V3.1" "Pp3c2_24640V3.1" "Pp3c2_24723V3.1" "Pp3c2_24761V3.1" "Pp3c2_24840V3.1" "Pp3c2_24870V3.1" "Pp3c2_25000V3.1"
[820] "Pp3c2_25160V3.1" "Pp3c2_25170V3.1" "Pp3c2_25580V3.1" "Pp3c2_25620V3.1" "Pp3c2_25690V3.1" "Pp3c2_25720V3.1" "Pp3c2_25890V3.1"
[827] "Pp3c2_25930V3.1" "Pp3c2_26060V3.1" "Pp3c2_26200V3.1" "Pp3c2_26250V3.1" "Pp3c2_26270V3.1" "Pp3c2_26320V3.1" "Pp3c2_26540V3.1"
[834] "Pp3c2_26550V3.1" "Pp3c2_26650V3.1" "Pp3c2_26700V3.1" "Pp3c2_26720V3.1" "Pp3c2_26970V3.1" "Pp3c2_27180V3.1" "Pp3c2_27330V3.1"
[841] "Pp3c2_27340V3.1" "Pp3c2_27350V3.1" "Pp3c2_27440V3.1" "Pp3c2_27480V3.1" "Pp3c2_27510V3.1" "Pp3c2_27540V3.1" "Pp3c2_27550V3.1"
[848] "Pp3c2_27590V3.1" "Pp3c2_27820V3.1" "Pp3c2_27910V3.1" "Pp3c2_27940V3.1" "Pp3c2_27970V3.1" "Pp3c2_27980V3.1" "Pp3c2_28030V3.1"
[855] "Pp3c2_28040V3.1" "Pp3c2_28130V3.1" "Pp3c2_28140V3.1" "Pp3c2_28162V3.1" "Pp3c2_28180V3.1" "Pp3c2_28380V3.1" "Pp3c2_28420V3.1"
[862] "Pp3c2_28540V3.1" "Pp3c2_28550V3.1" "Pp3c2_28570V3.1" "Pp3c2_28690V3.1" "Pp3c2_28870V3.1" "Pp3c2_29040V3.1" "Pp3c2_29249V3.1"
[869] "Pp3c2_29290V3.1" "Pp3c2_29500V3.1" "Pp3c2_29800V3.1" "Pp3c2_29840V3.1" "Pp3c2_30030V3.1" "Pp3c2_30040V3.1" "Pp3c2_30060V3.1"
[876] "Pp3c2_30250V3.1" "Pp3c2_30340V3.1" "Pp3c2_30370V3.1" "Pp3c2_30390V3.1" "Pp3c2_30510V3.1" "Pp3c2_30530V3.1" "Pp3c2_30580V3.1"
[883] "Pp3c2_30600V3.1" "Pp3c2_30610V3.1" "Pp3c2_30620V3.1" "Pp3c2_30630V3.1" "Pp3c2_30720V3.1" "Pp3c2_30770V3.1" "Pp3c2_30860V3.1"
[890] "Pp3c2_30940V3.1" "Pp3c2_30970V3.1" "Pp3c2_30980V3.1" "Pp3c2_31241V3.1" "Pp3c2_31270V3.1" "Pp3c2_31280V3.1" "Pp3c2_31330V3.1"
[897] "Pp3c2_31470V3.1" "Pp3c2_31540V3.1" "Pp3c2_31580V3.1" "Pp3c2_31590V3.1" "Pp3c2_31610V3.1" "Pp3c2_31930V3.1" "Pp3c2_32270V3.1"
[904] "Pp3c2_32310V3.1" "Pp3c2_32320V3.1" "Pp3c2_32400V3.1" "Pp3c2_32540V3.1" "Pp3c2_32600V3.1" "Pp3c2_32610V3.1" "Pp3c2_32690V3.1"
[911] "Pp3c2_32740V3.1" "Pp3c2_32770V3.1" "Pp3c2_32860V3.1" "Pp3c2_32990V3.1" "Pp3c2_33330V3.1" "Pp3c2_33430V3.1" "Pp3c2_33800V3.1"
[918] "Pp3c2_33890V3.1" "Pp3c2_33980V3.1" "Pp3c2_34110V3.1" "Pp3c2_34120V3.1" "Pp3c2_34130V3.1" "Pp3c2_34270V3.1" "Pp3c2_34310V3.1"
[925] "Pp3c2_34540V3.1" "Pp3c2_34550V3.1" "Pp3c2_34630V3.1" "Pp3c2_34670V3.1" "Pp3c2_34780V3.1" "Pp3c2_34820V3.1" "Pp3c2_34830V3.1"
[932] "Pp3c2_34890V3.1" "Pp3c2_34930V3.1" "Pp3c2_35010V3.1" "Pp3c2_35170V3.1" "Pp3c2_35200V3.1" "Pp3c2_35250V3.1" "Pp3c2_35530V3.1"
[939] "Pp3c2_35700V3.1" "Pp3c2_35740V3.1" "Pp3c2_35800V3.1" "Pp3c2_35870V3.1" "Pp3c2_35910V3.1" "Pp3c2_35930V3.1" "Pp3c2_35940V3.1"
[946] "Pp3c2_35950V3.1" "Pp3c2_36100V3.1" "Pp3c2_36220V3.1" "Pp3c2_36460V3.1" "Pp3c2_36480V3.1" "Pp3c2_36570V3.1" "Pp3c2_36790V3.1"
[953] "Pp3c2_36860V3.1" "Pp3c2_36990V3.1" "Pp3c2_37190V3.1" "Pp3c2_37210V3.1" "Pp3c2_37290V3.1" "Pp3c2_37299V3.1" "Pp3c2_37310V3.1"
[960] "Pp3c2_37670V3.1" "Pp3c2_37790V3.1" "Pp3c2_37900V3.1" "Pp3c2_37920V3.1" "Pp3c2_37990V3.1" "Pp3c2_38020V3.1" "Pp3c2_38120V3.1"
[967] "Pp3c2_38140V3.1" "Pp3c2_38160V3.1" "Pp3c2_38210V3.1" "Pp3c3_240V3.1" "Pp3c3_330V3.1" "Pp3c3_340V3.1" "Pp3c3_430V3.1"
[974] "Pp3c3_490V3.1" "Pp3c3_690V3.1" "Pp3c3_810V3.1" "Pp3c3_884V3.1" "Pp3c3_950V3.1" "Pp3c3_1020V3.1" "Pp3c3_1090V3.1"
[981] "Pp3c3_1160V3.1" "Pp3c3_1164V3.1" "Pp3c3_1500V3.1" "Pp3c3_1630V3.1" "Pp3c3_1700V3.1" "Pp3c3_1740V3.1" "Pp3c3_1750V3.1"
[988] "Pp3c3_1820V3.1" "Pp3c3_1910V3.1" "Pp3c3_2100V3.1" "Pp3c3_2130V3.1" "Pp3c3_2140V3.1" "Pp3c3_2240V3.1" "Pp3c3_2290V3.1"
[995] "Pp3c3_2380V3.1" "Pp3c3_2450V3.1" "Pp3c3_2620V3.1" "Pp3c3_2690V3.1" "Pp3c3_2730V3.1" "Pp3c3_2740V3.1"
[ reached getOption("max.print") -- omitted 6377 entries ]
[1] "DEGs edgeR"
[1] 13555
[1] "DEGs deseq2"
[1] 11922
[1] "DEGs noiseq"
[1] 7773
[1] "DEGs noiseqbio"
[1] 8967
[1] "DEGs intersection without direction check (three methods)"
[1] 7726
[1] "Pp3c1_40V3.1" "Pp3c1_200V3.1" "Pp3c1_370V3.1" "Pp3c1_470V3.1" "Pp3c1_540V3.1" "Pp3c1_580V3.1" "Pp3c1_680V3.1"
[8] "Pp3c1_690V3.1" "Pp3c1_890V3.1" "Pp3c1_900V3.1" "Pp3c1_950V3.1" "Pp3c1_1000V3.1" "Pp3c1_1160V3.1" "Pp3c1_1260V3.1"
[15] "Pp3c1_1330V3.1" "Pp3c1_1360V3.1" "Pp3c1_1390V3.1" "Pp3c1_1570V3.1" "Pp3c1_1800V3.1" "Pp3c1_1810V3.1" "Pp3c1_1860V3.1"
[22] "Pp3c1_1870V3.1" "Pp3c1_1940V3.1" "Pp3c1_2170V3.1" "Pp3c1_2210V3.1" "Pp3c1_2220V3.1" "Pp3c1_2420V3.1" "Pp3c1_2540V3.1"
[29] "Pp3c1_2740V3.1" "Pp3c1_2920V3.1" "Pp3c1_2980V3.1" "Pp3c1_3040V3.1" "Pp3c1_3160V3.1" "Pp3c1_3180V3.1" "Pp3c1_3200V3.1"
[36] "Pp3c1_3210V3.1" "Pp3c1_3220V3.1" "Pp3c1_3300V3.1" "Pp3c1_3500V3.1" "Pp3c1_3590V3.1" "Pp3c1_3610V3.1" "Pp3c1_3700V3.1"
[43] "Pp3c1_3730V3.1" "Pp3c1_3750V3.1" "Pp3c1_3890V3.1" "Pp3c1_3930V3.1" "Pp3c1_4010V3.1" "Pp3c1_4030V3.1" "Pp3c1_4050V3.1"
[50] "Pp3c1_4140V3.1" "Pp3c1_4180V3.1" "Pp3c1_4270V3.1" "Pp3c1_4300V3.1" "Pp3c1_4350V3.1" "Pp3c1_4470V3.1" "Pp3c1_4600V3.1"
[57] "Pp3c1_4750V3.1" "Pp3c1_4990V3.1" "Pp3c1_5050V3.1" "Pp3c1_5280V3.1" "Pp3c1_5300V3.1" "Pp3c1_5320V3.1" "Pp3c1_5460V3.1"
[64] "Pp3c1_5570V3.1" "Pp3c1_5800V3.1" "Pp3c1_5820V3.1" "Pp3c1_5850V3.1" "Pp3c1_5870V3.1" "Pp3c1_6020V3.1" "Pp3c1_6050V3.1"
[71] "Pp3c1_6090V3.1" "Pp3c1_6110V3.1" "Pp3c1_6272V3.1" "Pp3c1_6280V3.1" "Pp3c1_6360V3.1" "Pp3c1_6450V3.1" "Pp3c1_6470V3.1"
[78] "Pp3c1_6480V3.1" "Pp3c1_6500V3.1" "Pp3c1_6570V3.1" "Pp3c1_6640V3.1" "Pp3c1_6750V3.1" "Pp3c1_6930V3.1" "Pp3c1_6980V3.1"
[85] "Pp3c1_7030V3.1" "Pp3c1_7160V3.1" "Pp3c1_7170V3.1" "Pp3c1_7300V3.1" "Pp3c1_7370V3.1" "Pp3c1_7380V3.1" "Pp3c1_7450V3.1"
[92] "Pp3c1_7500V3.1" "Pp3c1_7520V3.1" "Pp3c1_7540V3.1" "Pp3c1_7590V3.1" "Pp3c1_7710V3.1" "Pp3c1_7720V3.1" "Pp3c1_7810V3.1"
[99] "Pp3c1_7830V3.1" "Pp3c1_7880V3.1" "Pp3c1_7910V3.1" "Pp3c1_7950V3.1" "Pp3c1_8060V3.1" "Pp3c1_8080V3.1" "Pp3c1_8110V3.1"
[106] "Pp3c1_8170V3.1" "Pp3c1_8190V3.1" "Pp3c1_8280V3.1" "Pp3c1_8440V3.1" "Pp3c1_8530V3.1" "Pp3c1_8550V3.1" "Pp3c1_8870V3.1"
[113] "Pp3c1_8890V3.1" "Pp3c1_9180V3.1" "Pp3c1_9250V3.1" "Pp3c1_9290V3.1" "Pp3c1_9320V3.1" "Pp3c1_9560V3.1" "Pp3c1_9600V3.1"
[120] "Pp3c1_9630V3.1" "Pp3c1_9790V3.1" "Pp3c1_9860V3.1" "Pp3c1_9970V3.1" "Pp3c1_10010V3.1" "Pp3c1_10040V3.1" "Pp3c1_10080V3.1"
[127] "Pp3c1_10090V3.1" "Pp3c1_10100V3.1" "Pp3c1_10180V3.1" "Pp3c1_10200V3.1" "Pp3c1_10220V3.1" "Pp3c1_10400V3.1" "Pp3c1_10470V3.1"
[134] "Pp3c1_10540V3.1" "Pp3c1_10570V3.1" "Pp3c1_10620V3.1" "Pp3c1_10810V3.1" "Pp3c1_10880V3.1" "Pp3c1_10970V3.1" "Pp3c1_11030V3.1"
[141] "Pp3c1_11050V3.1" "Pp3c1_11090V3.1" "Pp3c1_11190V3.1" "Pp3c1_11980V3.1" "Pp3c1_12020V3.1" "Pp3c1_12100V3.1" "Pp3c1_12120V3.1"
[148] "Pp3c1_12140V3.1" "Pp3c1_12470V3.1" "Pp3c1_12610V3.1" "Pp3c1_12630V3.1" "Pp3c1_12730V3.1" "Pp3c1_12790V3.1" "Pp3c1_12810V3.1"
[155] "Pp3c1_12850V3.1" "Pp3c1_12860V3.1" "Pp3c1_12940V3.1" "Pp3c1_13120V3.1" "Pp3c1_13170V3.1" "Pp3c1_13308V3.1" "Pp3c1_13430V3.1"
[162] "Pp3c1_13570V3.1" "Pp3c1_13640V3.1" "Pp3c1_13670V3.1" "Pp3c1_13671V3.1" "Pp3c1_13830V3.1" "Pp3c1_13910V3.1" "Pp3c1_14230V3.1"
[169] "Pp3c1_14330V3.1" "Pp3c1_14380V3.1" "Pp3c1_14670V3.1" "Pp3c1_14740V3.1" "Pp3c1_14760V3.1" "Pp3c1_14770V3.1" "Pp3c1_14800V3.1"
[176] "Pp3c1_14870V3.1" "Pp3c1_14910V3.1" "Pp3c1_14980V3.1" "Pp3c1_15010V3.1" "Pp3c1_15100V3.1" "Pp3c1_15110V3.1" "Pp3c1_15150V3.1"
[183] "Pp3c1_15160V3.1" "Pp3c1_15210V3.1" "Pp3c1_15400V3.1" "Pp3c1_15410V3.1" "Pp3c1_15460V3.1" "Pp3c1_15490V3.1" "Pp3c1_15560V3.1"
[190] "Pp3c1_15690V3.1" "Pp3c1_15730V3.1" "Pp3c1_15750V3.1" "Pp3c1_15940V3.1" "Pp3c1_16170V3.1" "Pp3c1_16250V3.1" "Pp3c1_16260V3.1"
[197] "Pp3c1_16500V3.1" "Pp3c1_16600V3.1" "Pp3c1_16780V3.1" "Pp3c1_16840V3.1" "Pp3c1_16850V3.1" "Pp3c1_16900V3.1" "Pp3c1_16980V3.1"
[204] "Pp3c1_17080V3.1" "Pp3c1_17220V3.1" "Pp3c1_17370V3.1" "Pp3c1_17870V3.1" "Pp3c1_18130V3.1" "Pp3c1_18260V3.1" "Pp3c1_18420V3.1"
[211] "Pp3c1_18440V3.1" "Pp3c1_18460V3.1" "Pp3c1_18530V3.1" "Pp3c1_18830V3.1" "Pp3c1_18860V3.1" "Pp3c1_18910V3.1" "Pp3c1_18940V3.1"
[218] "Pp3c1_19060V3.1" "Pp3c1_19176V3.1" "Pp3c1_19210V3.1" "Pp3c1_19230V3.1" "Pp3c1_19240V3.1" "Pp3c1_19370V3.1" "Pp3c1_19400V3.1"
[225] "Pp3c1_19590V3.1" "Pp3c1_19660V3.1" "Pp3c1_20010V3.1" "Pp3c1_20040V3.1" "Pp3c1_20050V3.1" "Pp3c1_20280V3.1" "Pp3c1_20310V3.1"
[232] "Pp3c1_20350V3.1" "Pp3c1_20610V3.1" "Pp3c1_20640V3.1" "Pp3c1_20690V3.1" "Pp3c1_20700V3.1" "Pp3c1_20753V3.1" "Pp3c1_20770V3.1"
[239] "Pp3c1_20870V3.1" "Pp3c1_20880V3.1" "Pp3c1_20960V3.1" "Pp3c1_20980V3.1" "Pp3c1_21050V3.1" "Pp3c1_21160V3.1" "Pp3c1_21200V3.1"
[246] "Pp3c1_21230V3.1" "Pp3c1_21270V3.1" "Pp3c1_21290V3.1" "Pp3c1_21360V3.1" "Pp3c1_21400V3.1" "Pp3c1_21480V3.1" "Pp3c1_21510V3.1"
[253] "Pp3c1_21540V3.1" "Pp3c1_21550V3.1" "Pp3c1_21620V3.1" "Pp3c1_21650V3.1" "Pp3c1_21730V3.1" "Pp3c1_21760V3.1" "Pp3c1_21810V3.1"
[260] "Pp3c1_21850V3.1" "Pp3c1_21890V3.1" "Pp3c1_21920V3.1" "Pp3c1_22090V3.1" "Pp3c1_22120V3.1" "Pp3c1_22260V3.1" "Pp3c1_22360V3.1"
[267] "Pp3c1_22450V3.1" "Pp3c1_22520V3.1" "Pp3c1_22540V3.1" "Pp3c1_22560V3.1" "Pp3c1_22590V3.1" "Pp3c1_22690V3.1" "Pp3c1_22710V3.1"
[274] "Pp3c1_22820V3.1" "Pp3c1_22900V3.1" "Pp3c1_22950V3.1" "Pp3c1_23000V3.1" "Pp3c1_23010V3.1" "Pp3c1_23040V3.1" "Pp3c1_23190V3.1"
[281] "Pp3c1_23250V3.1" "Pp3c1_23260V3.1" "Pp3c1_23300V3.1" "Pp3c1_23410V3.1" "Pp3c1_23490V3.1" "Pp3c1_23520V3.1" "Pp3c1_23590V3.1"
[288] "Pp3c1_23600V3.1" "Pp3c1_23750V3.1" "Pp3c1_23850V3.1" "Pp3c1_23900V3.1" "Pp3c1_23920V3.1" "Pp3c1_23930V3.1" "Pp3c1_23960V3.1"
[295] "Pp3c1_23970V3.1" "Pp3c1_24000V3.1" "Pp3c1_24120V3.1" "Pp3c1_24280V3.1" "Pp3c1_24300V3.1" "Pp3c1_24350V3.1" "Pp3c1_24440V3.1"
[302] "Pp3c1_24500V3.1" "Pp3c1_24560V3.1" "Pp3c1_24600V3.1" "Pp3c1_24790V3.1" "Pp3c1_24820V3.1" "Pp3c1_24950V3.1" "Pp3c1_25000V3.1"
[309] "Pp3c1_25070V3.1" "Pp3c1_25080V3.1" "Pp3c1_25290V3.1" "Pp3c1_25400V3.1" "Pp3c1_25410V3.1" "Pp3c1_25450V3.1" "Pp3c1_25570V3.1"
[316] "Pp3c1_25640V3.1" "Pp3c1_25700V3.1" "Pp3c1_25750V3.1" "Pp3c1_25770V3.1" "Pp3c1_25820V3.1" "Pp3c1_25850V3.1" "Pp3c1_25920V3.1"
[323] "Pp3c1_25940V3.1" "Pp3c1_25970V3.1" "Pp3c1_26200V3.1" "Pp3c1_26270V3.1" "Pp3c1_26350V3.1" "Pp3c1_26720V3.1" "Pp3c1_26730V3.1"
[330] "Pp3c1_26740V3.1" "Pp3c1_26780V3.1" "Pp3c1_27020V3.1" "Pp3c1_27160V3.1" "Pp3c1_27230V3.1" "Pp3c1_27440V3.1" "Pp3c1_27510V3.1"
[337] "Pp3c1_27630V3.1" "Pp3c1_27830V3.1" "Pp3c1_27870V3.1" "Pp3c1_27990V3.1" "Pp3c1_28060V3.1" "Pp3c1_28200V3.1" "Pp3c1_28340V3.1"
[344] "Pp3c1_28370V3.1" "Pp3c1_28390V3.1" "Pp3c1_28430V3.1" "Pp3c1_28480V3.1" "Pp3c1_28680V3.1" "Pp3c1_28690V3.1" "Pp3c1_28750V3.1"
[351] "Pp3c1_28760V3.1" "Pp3c1_29030V3.1" "Pp3c1_29050V3.1" "Pp3c1_29070V3.1" "Pp3c1_29090V3.1" "Pp3c1_29130V3.1" "Pp3c1_29160V3.1"
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[883] "Pp3c2_27590V3.1" "Pp3c2_27820V3.1" "Pp3c2_27910V3.1" "Pp3c2_27930V3.1" "Pp3c2_27940V3.1" "Pp3c2_27970V3.1" "Pp3c2_27980V3.1"
[890] "Pp3c2_28030V3.1" "Pp3c2_28040V3.1" "Pp3c2_28130V3.1" "Pp3c2_28140V3.1" "Pp3c2_28162V3.1" "Pp3c2_28180V3.1" "Pp3c2_28380V3.1"
[897] "Pp3c2_28420V3.1" "Pp3c2_28540V3.1" "Pp3c2_28550V3.1" "Pp3c2_28570V3.1" "Pp3c2_28690V3.1" "Pp3c2_28870V3.1" "Pp3c2_29040V3.1"
[904] "Pp3c2_29249V3.1" "Pp3c2_29290V3.1" "Pp3c2_29500V3.1" "Pp3c2_29800V3.1" "Pp3c2_29840V3.1" "Pp3c2_30030V3.1" "Pp3c2_30040V3.1"
[911] "Pp3c2_30060V3.1" "Pp3c2_30250V3.1" "Pp3c2_30270V3.1" "Pp3c2_30340V3.1" "Pp3c2_30370V3.1" "Pp3c2_30390V3.1" "Pp3c2_30510V3.1"
[918] "Pp3c2_30530V3.1" "Pp3c2_30580V3.1" "Pp3c2_30600V3.1" "Pp3c2_30610V3.1" "Pp3c2_30620V3.1" "Pp3c2_30630V3.1" "Pp3c2_30720V3.1"
[925] "Pp3c2_30770V3.1" "Pp3c2_30860V3.1" "Pp3c2_30940V3.1" "Pp3c2_30970V3.1" "Pp3c2_30980V3.1" "Pp3c2_31241V3.1" "Pp3c2_31270V3.1"
[932] "Pp3c2_31280V3.1" "Pp3c2_31330V3.1" "Pp3c2_31470V3.1" "Pp3c2_31540V3.1" "Pp3c2_31580V3.1" "Pp3c2_31590V3.1" "Pp3c2_31610V3.1"
[939] "Pp3c2_31930V3.1" "Pp3c2_32270V3.1" "Pp3c2_32310V3.1" "Pp3c2_32320V3.1" "Pp3c2_32400V3.1" "Pp3c2_32540V3.1" "Pp3c2_32600V3.1"
[946] "Pp3c2_32610V3.1" "Pp3c2_32690V3.1" "Pp3c2_32740V3.1" "Pp3c2_32770V3.1" "Pp3c2_32860V3.1" "Pp3c2_32990V3.1" "Pp3c2_33330V3.1"
[953] "Pp3c2_33430V3.1" "Pp3c2_33800V3.1" "Pp3c2_33890V3.1" "Pp3c2_33980V3.1" "Pp3c2_34110V3.1" "Pp3c2_34120V3.1" "Pp3c2_34130V3.1"
[960] "Pp3c2_34270V3.1" "Pp3c2_34310V3.1" "Pp3c2_34320V3.1" "Pp3c2_34540V3.1" "Pp3c2_34550V3.1" "Pp3c2_34630V3.1" "Pp3c2_34670V3.1"
[967] "Pp3c2_34780V3.1" "Pp3c2_34820V3.1" "Pp3c2_34830V3.1" "Pp3c2_34890V3.1" "Pp3c2_34930V3.1" "Pp3c2_35010V3.1" "Pp3c2_35170V3.1"
[974] "Pp3c2_35200V3.1" "Pp3c2_35250V3.1" "Pp3c2_35530V3.1" "Pp3c2_35700V3.1" "Pp3c2_35740V3.1" "Pp3c2_35800V3.1" "Pp3c2_35870V3.1"
[981] "Pp3c2_35910V3.1" "Pp3c2_35930V3.1" "Pp3c2_35940V3.1" "Pp3c2_35950V3.1" "Pp3c2_36100V3.1" "Pp3c2_36220V3.1" "Pp3c2_36460V3.1"
[988] "Pp3c2_36480V3.1" "Pp3c2_36570V3.1" "Pp3c2_36790V3.1" "Pp3c2_36860V3.1" "Pp3c2_36990V3.1" "Pp3c2_37190V3.1" "Pp3c2_37210V3.1"
[995] "Pp3c2_37290V3.1" "Pp3c2_37299V3.1" "Pp3c2_37310V3.1" "Pp3c2_37670V3.1" "Pp3c2_37690V3.1" "Pp3c2_37790V3.1"
[ reached getOption("max.print") -- omitted 6726 entries ]
[1] "DEGs intersection with direction check"
[1] 7726
[1] "Pp3c1_40V3.1" "Pp3c1_200V3.1" "Pp3c1_370V3.1" "Pp3c1_470V3.1" "Pp3c1_540V3.1" "Pp3c1_580V3.1" "Pp3c1_680V3.1"
[8] "Pp3c1_690V3.1" "Pp3c1_890V3.1" "Pp3c1_900V3.1" "Pp3c1_950V3.1" "Pp3c1_1000V3.1" "Pp3c1_1160V3.1" "Pp3c1_1260V3.1"
[15] "Pp3c1_1330V3.1" "Pp3c1_1360V3.1" "Pp3c1_1390V3.1" "Pp3c1_1570V3.1" "Pp3c1_1800V3.1" "Pp3c1_1810V3.1" "Pp3c1_1860V3.1"
[22] "Pp3c1_1870V3.1" "Pp3c1_1940V3.1" "Pp3c1_2170V3.1" "Pp3c1_2210V3.1" "Pp3c1_2220V3.1" "Pp3c1_2420V3.1" "Pp3c1_2540V3.1"
[29] "Pp3c1_2740V3.1" "Pp3c1_2920V3.1" "Pp3c1_2980V3.1" "Pp3c1_3040V3.1" "Pp3c1_3160V3.1" "Pp3c1_3180V3.1" "Pp3c1_3200V3.1"
[36] "Pp3c1_3210V3.1" "Pp3c1_3220V3.1" "Pp3c1_3300V3.1" "Pp3c1_3500V3.1" "Pp3c1_3590V3.1" "Pp3c1_3610V3.1" "Pp3c1_3700V3.1"
[43] "Pp3c1_3730V3.1" "Pp3c1_3750V3.1" "Pp3c1_3890V3.1" "Pp3c1_3930V3.1" "Pp3c1_4010V3.1" "Pp3c1_4030V3.1" "Pp3c1_4050V3.1"
[50] "Pp3c1_4140V3.1" "Pp3c1_4180V3.1" "Pp3c1_4270V3.1" "Pp3c1_4300V3.1" "Pp3c1_4350V3.1" "Pp3c1_4470V3.1" "Pp3c1_4600V3.1"
[57] "Pp3c1_4750V3.1" "Pp3c1_4990V3.1" "Pp3c1_5050V3.1" "Pp3c1_5280V3.1" "Pp3c1_5300V3.1" "Pp3c1_5320V3.1" "Pp3c1_5460V3.1"
[64] "Pp3c1_5570V3.1" "Pp3c1_5800V3.1" "Pp3c1_5820V3.1" "Pp3c1_5850V3.1" "Pp3c1_5870V3.1" "Pp3c1_6020V3.1" "Pp3c1_6050V3.1"
[71] "Pp3c1_6090V3.1" "Pp3c1_6110V3.1" "Pp3c1_6272V3.1" "Pp3c1_6280V3.1" "Pp3c1_6360V3.1" "Pp3c1_6450V3.1" "Pp3c1_6470V3.1"
[78] "Pp3c1_6480V3.1" "Pp3c1_6500V3.1" "Pp3c1_6570V3.1" "Pp3c1_6640V3.1" "Pp3c1_6750V3.1" "Pp3c1_6930V3.1" "Pp3c1_6980V3.1"
[85] "Pp3c1_7030V3.1" "Pp3c1_7160V3.1" "Pp3c1_7170V3.1" "Pp3c1_7300V3.1" "Pp3c1_7370V3.1" "Pp3c1_7380V3.1" "Pp3c1_7450V3.1"
[92] "Pp3c1_7500V3.1" "Pp3c1_7520V3.1" "Pp3c1_7540V3.1" "Pp3c1_7590V3.1" "Pp3c1_7710V3.1" "Pp3c1_7720V3.1" "Pp3c1_7810V3.1"
[99] "Pp3c1_7830V3.1" "Pp3c1_7880V3.1" "Pp3c1_7910V3.1" "Pp3c1_7950V3.1" "Pp3c1_8060V3.1" "Pp3c1_8080V3.1" "Pp3c1_8110V3.1"
[106] "Pp3c1_8170V3.1" "Pp3c1_8190V3.1" "Pp3c1_8280V3.1" "Pp3c1_8440V3.1" "Pp3c1_8530V3.1" "Pp3c1_8550V3.1" "Pp3c1_8870V3.1"
[113] "Pp3c1_8890V3.1" "Pp3c1_9180V3.1" "Pp3c1_9250V3.1" "Pp3c1_9290V3.1" "Pp3c1_9320V3.1" "Pp3c1_9560V3.1" "Pp3c1_9600V3.1"
[120] "Pp3c1_9630V3.1" "Pp3c1_9790V3.1" "Pp3c1_9860V3.1" "Pp3c1_9970V3.1" "Pp3c1_10010V3.1" "Pp3c1_10040V3.1" "Pp3c1_10080V3.1"
[127] "Pp3c1_10090V3.1" "Pp3c1_10100V3.1" "Pp3c1_10180V3.1" "Pp3c1_10200V3.1" "Pp3c1_10220V3.1" "Pp3c1_10400V3.1" "Pp3c1_10470V3.1"
[134] "Pp3c1_10540V3.1" "Pp3c1_10570V3.1" "Pp3c1_10620V3.1" "Pp3c1_10810V3.1" "Pp3c1_10880V3.1" "Pp3c1_10970V3.1" "Pp3c1_11030V3.1"
[141] "Pp3c1_11050V3.1" "Pp3c1_11090V3.1" "Pp3c1_11190V3.1" "Pp3c1_11980V3.1" "Pp3c1_12020V3.1" "Pp3c1_12100V3.1" "Pp3c1_12120V3.1"
[148] "Pp3c1_12140V3.1" "Pp3c1_12470V3.1" "Pp3c1_12610V3.1" "Pp3c1_12630V3.1" "Pp3c1_12730V3.1" "Pp3c1_12790V3.1" "Pp3c1_12810V3.1"
[155] "Pp3c1_12850V3.1" "Pp3c1_12860V3.1" "Pp3c1_12940V3.1" "Pp3c1_13120V3.1" "Pp3c1_13170V3.1" "Pp3c1_13308V3.1" "Pp3c1_13430V3.1"
[162] "Pp3c1_13570V3.1" "Pp3c1_13640V3.1" "Pp3c1_13670V3.1" "Pp3c1_13671V3.1" "Pp3c1_13830V3.1" "Pp3c1_13910V3.1" "Pp3c1_14230V3.1"
[169] "Pp3c1_14330V3.1" "Pp3c1_14380V3.1" "Pp3c1_14670V3.1" "Pp3c1_14740V3.1" "Pp3c1_14760V3.1" "Pp3c1_14770V3.1" "Pp3c1_14800V3.1"
[176] "Pp3c1_14870V3.1" "Pp3c1_14910V3.1" "Pp3c1_14980V3.1" "Pp3c1_15010V3.1" "Pp3c1_15100V3.1" "Pp3c1_15110V3.1" "Pp3c1_15150V3.1"
[183] "Pp3c1_15160V3.1" "Pp3c1_15210V3.1" "Pp3c1_15400V3.1" "Pp3c1_15410V3.1" "Pp3c1_15460V3.1" "Pp3c1_15490V3.1" "Pp3c1_15560V3.1"
[190] "Pp3c1_15690V3.1" "Pp3c1_15730V3.1" "Pp3c1_15750V3.1" "Pp3c1_15940V3.1" "Pp3c1_16170V3.1" "Pp3c1_16250V3.1" "Pp3c1_16260V3.1"
[197] "Pp3c1_16500V3.1" "Pp3c1_16600V3.1" "Pp3c1_16780V3.1" "Pp3c1_16840V3.1" "Pp3c1_16850V3.1" "Pp3c1_16900V3.1" "Pp3c1_16980V3.1"
[204] "Pp3c1_17080V3.1" "Pp3c1_17220V3.1" "Pp3c1_17370V3.1" "Pp3c1_17870V3.1" "Pp3c1_18130V3.1" "Pp3c1_18260V3.1" "Pp3c1_18420V3.1"
[211] "Pp3c1_18440V3.1" "Pp3c1_18460V3.1" "Pp3c1_18530V3.1" "Pp3c1_18830V3.1" "Pp3c1_18860V3.1" "Pp3c1_18910V3.1" "Pp3c1_18940V3.1"
[218] "Pp3c1_19060V3.1" "Pp3c1_19176V3.1" "Pp3c1_19210V3.1" "Pp3c1_19230V3.1" "Pp3c1_19240V3.1" "Pp3c1_19370V3.1" "Pp3c1_19400V3.1"
[225] "Pp3c1_19590V3.1" "Pp3c1_19660V3.1" "Pp3c1_20010V3.1" "Pp3c1_20040V3.1" "Pp3c1_20050V3.1" "Pp3c1_20280V3.1" "Pp3c1_20310V3.1"
[232] "Pp3c1_20350V3.1" "Pp3c1_20610V3.1" "Pp3c1_20640V3.1" "Pp3c1_20690V3.1" "Pp3c1_20700V3.1" "Pp3c1_20753V3.1" "Pp3c1_20770V3.1"
[239] "Pp3c1_20870V3.1" "Pp3c1_20880V3.1" "Pp3c1_20960V3.1" "Pp3c1_20980V3.1" "Pp3c1_21050V3.1" "Pp3c1_21160V3.1" "Pp3c1_21200V3.1"
[246] "Pp3c1_21230V3.1" "Pp3c1_21270V3.1" "Pp3c1_21290V3.1" "Pp3c1_21360V3.1" "Pp3c1_21400V3.1" "Pp3c1_21480V3.1" "Pp3c1_21510V3.1"
[253] "Pp3c1_21540V3.1" "Pp3c1_21550V3.1" "Pp3c1_21620V3.1" "Pp3c1_21650V3.1" "Pp3c1_21730V3.1" "Pp3c1_21760V3.1" "Pp3c1_21810V3.1"
[260] "Pp3c1_21850V3.1" "Pp3c1_21890V3.1" "Pp3c1_21920V3.1" "Pp3c1_22090V3.1" "Pp3c1_22120V3.1" "Pp3c1_22260V3.1" "Pp3c1_22360V3.1"
[267] "Pp3c1_22450V3.1" "Pp3c1_22520V3.1" "Pp3c1_22540V3.1" "Pp3c1_22560V3.1" "Pp3c1_22590V3.1" "Pp3c1_22690V3.1" "Pp3c1_22710V3.1"
[274] "Pp3c1_22820V3.1" "Pp3c1_22900V3.1" "Pp3c1_22950V3.1" "Pp3c1_23000V3.1" "Pp3c1_23010V3.1" "Pp3c1_23040V3.1" "Pp3c1_23190V3.1"
[281] "Pp3c1_23250V3.1" "Pp3c1_23260V3.1" "Pp3c1_23300V3.1" "Pp3c1_23410V3.1" "Pp3c1_23490V3.1" "Pp3c1_23520V3.1" "Pp3c1_23590V3.1"
[288] "Pp3c1_23600V3.1" "Pp3c1_23750V3.1" "Pp3c1_23850V3.1" "Pp3c1_23900V3.1" "Pp3c1_23920V3.1" "Pp3c1_23930V3.1" "Pp3c1_23960V3.1"
[295] "Pp3c1_23970V3.1" "Pp3c1_24000V3.1" "Pp3c1_24120V3.1" "Pp3c1_24280V3.1" "Pp3c1_24300V3.1" "Pp3c1_24350V3.1" "Pp3c1_24440V3.1"
[302] "Pp3c1_24500V3.1" "Pp3c1_24560V3.1" "Pp3c1_24600V3.1" "Pp3c1_24790V3.1" "Pp3c1_24820V3.1" "Pp3c1_24950V3.1" "Pp3c1_25000V3.1"
[309] "Pp3c1_25070V3.1" "Pp3c1_25080V3.1" "Pp3c1_25290V3.1" "Pp3c1_25400V3.1" "Pp3c1_25410V3.1" "Pp3c1_25450V3.1" "Pp3c1_25570V3.1"
[316] "Pp3c1_25640V3.1" "Pp3c1_25700V3.1" "Pp3c1_25750V3.1" "Pp3c1_25770V3.1" "Pp3c1_25820V3.1" "Pp3c1_25850V3.1" "Pp3c1_25920V3.1"
[323] "Pp3c1_25940V3.1" "Pp3c1_25970V3.1" "Pp3c1_26200V3.1" "Pp3c1_26270V3.1" "Pp3c1_26350V3.1" "Pp3c1_26720V3.1" "Pp3c1_26730V3.1"
[330] "Pp3c1_26740V3.1" "Pp3c1_26780V3.1" "Pp3c1_27020V3.1" "Pp3c1_27160V3.1" "Pp3c1_27230V3.1" "Pp3c1_27440V3.1" "Pp3c1_27510V3.1"
[337] "Pp3c1_27630V3.1" "Pp3c1_27830V3.1" "Pp3c1_27870V3.1" "Pp3c1_27990V3.1" "Pp3c1_28060V3.1" "Pp3c1_28200V3.1" "Pp3c1_28340V3.1"
[344] "Pp3c1_28370V3.1" "Pp3c1_28390V3.1" "Pp3c1_28430V3.1" "Pp3c1_28480V3.1" "Pp3c1_28680V3.1" "Pp3c1_28690V3.1" "Pp3c1_28750V3.1"
[351] "Pp3c1_28760V3.1" "Pp3c1_29030V3.1" "Pp3c1_29050V3.1" "Pp3c1_29070V3.1" "Pp3c1_29090V3.1" "Pp3c1_29130V3.1" "Pp3c1_29160V3.1"
[358] "Pp3c1_29300V3.1" "Pp3c1_29380V3.1" "Pp3c1_29390V3.1" "Pp3c1_29440V3.1" "Pp3c1_29460V3.1" "Pp3c1_29500V3.1" "Pp3c1_29560V3.1"
[365] "Pp3c1_29590V3.1" "Pp3c1_29600V3.1" "Pp3c1_29630V3.1" "Pp3c1_29650V3.1" "Pp3c1_29770V3.1" "Pp3c1_29970V3.1" "Pp3c1_30080V3.1"
[372] "Pp3c1_30090V3.1" "Pp3c1_30120V3.1" "Pp3c1_30150V3.1" "Pp3c1_30400V3.1" "Pp3c1_30410V3.1" "Pp3c1_30550V3.1" "Pp3c1_30570V3.1"
[379] "Pp3c1_30620V3.1" "Pp3c1_30640V3.1" "Pp3c1_30760V3.1" "Pp3c1_30790V3.1" "Pp3c1_30960V3.1" "Pp3c1_30990V3.1" "Pp3c1_31250V3.1"
[386] "Pp3c1_31280V3.1" "Pp3c1_31440V3.1" "Pp3c1_31540V3.1" "Pp3c1_31630V3.1" "Pp3c1_31680V3.1" "Pp3c1_31720V3.1" "Pp3c1_31730V3.1"
[393] "Pp3c1_31830V3.1" "Pp3c1_31850V3.1" "Pp3c1_31910V3.1" "Pp3c1_31930V3.1" "Pp3c1_32070V3.1" "Pp3c1_32090V3.1" "Pp3c1_32120V3.1"
[400] "Pp3c1_32170V3.1" "Pp3c1_32190V3.1" "Pp3c1_32200V3.1" "Pp3c1_32210V3.1" "Pp3c1_32230V3.1" "Pp3c1_32280V3.1" "Pp3c1_32320V3.1"
[407] "Pp3c1_32350V3.1" "Pp3c1_32440V3.1" "Pp3c1_32490V3.1" "Pp3c1_32520V3.1" "Pp3c1_32600V3.1" "Pp3c1_32740V3.1" "Pp3c1_32750V3.1"
[414] "Pp3c1_32760V3.1" "Pp3c1_32770V3.1" "Pp3c1_32910V3.1" "Pp3c1_32920V3.1" "Pp3c1_32960V3.1" "Pp3c1_33030V3.1" "Pp3c1_33050V3.1"
[421] "Pp3c1_33120V3.1" "Pp3c1_33150V3.1" "Pp3c1_33190V3.1" "Pp3c1_33300V3.1" "Pp3c1_33430V3.1" "Pp3c1_33460V3.1" "Pp3c1_33470V3.1"
[428] "Pp3c1_33480V3.1" "Pp3c1_33710V3.1" "Pp3c1_33790V3.1" "Pp3c1_33830V3.1" "Pp3c1_33890V3.1" "Pp3c1_34050V3.1" "Pp3c1_34210V3.1"
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[960] "Pp3c2_34270V3.1" "Pp3c2_34310V3.1" "Pp3c2_34320V3.1" "Pp3c2_34540V3.1" "Pp3c2_34550V3.1" "Pp3c2_34630V3.1" "Pp3c2_34670V3.1"
[967] "Pp3c2_34780V3.1" "Pp3c2_34820V3.1" "Pp3c2_34830V3.1" "Pp3c2_34890V3.1" "Pp3c2_34930V3.1" "Pp3c2_35010V3.1" "Pp3c2_35170V3.1"
[974] "Pp3c2_35200V3.1" "Pp3c2_35250V3.1" "Pp3c2_35530V3.1" "Pp3c2_35700V3.1" "Pp3c2_35740V3.1" "Pp3c2_35800V3.1" "Pp3c2_35870V3.1"
[981] "Pp3c2_35910V3.1" "Pp3c2_35930V3.1" "Pp3c2_35940V3.1" "Pp3c2_35950V3.1" "Pp3c2_36100V3.1" "Pp3c2_36220V3.1" "Pp3c2_36460V3.1"
[988] "Pp3c2_36480V3.1" "Pp3c2_36570V3.1" "Pp3c2_36790V3.1" "Pp3c2_36860V3.1" "Pp3c2_36990V3.1" "Pp3c2_37190V3.1" "Pp3c2_37210V3.1"
[995] "Pp3c2_37290V3.1" "Pp3c2_37299V3.1" "Pp3c2_37310V3.1" "Pp3c2_37670V3.1" "Pp3c2_37690V3.1" "Pp3c2_37790V3.1"
[ reached getOption("max.print") -- omitted 6726 entries ]
runs/RNA-Seq_analysis/DEGs/DEGs_0.9/WT_D_WT_L/DESeq2/WT_D vs. WT_L_11922_DESeq2_fdr.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/WT_D_WT_L/NOISeq/WT_D vs. WT_L_4189_NOISeq_nnorm_prob.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/WT_D_WT_L/NOISeq/WT_D vs. WT_L_7773_NOISeq_rpkm_prob.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/WT_D_WT_L/NOISeq/WT_D vs. WT_L_7801_NOISeq_tmm_prob.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/WT_D_WT_L/NOISeq/WT_D vs. WT_L_8967_NOISeqbio_rpkm_prob_seed_12345.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/WT_D_WT_L/NOISeq/WT_D vs. WT_L_9187_NOISeqbio_tmm_prob_seed_12345.tsv 0 → 100755
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