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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/cop_D_WT_L/cop_D_vs._WT_L_intersection_four_methods_6271.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/cop_D_WT_L/cop_D_vs._WT_L_intersection_four_methods_6271.tsv.filter_-1_1.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/cop_D_WT_L/cop_D_vs._WT_L_intersection_three_methods_6925.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/cop_D_WT_L/cop_D_vs._WT_L_intersection_three_methods_6925.tsv.filter_-1_1.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/cop_D_WT_L/edgeR/cop_D vs. WT_L_12738_edgeR_fdr.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/cop_D_cop_L/DEGpipe_cop_D vs. cop_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_D" "SampleNames: cop_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] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] gplots_3.1.1 edgeR_3.32.1 limma_3.46.0 pals_1.7
[5] gridExtra_2.3 sjmisc_2.8.7 magick_2.7.2 pheatmap_1.0.12
[9] RColorBrewer_1.1-2 ggplot2_3.3.3 DESeq2_1.30.1 SummarizedExperiment_1.20.0
[13] Biobase_2.50.0 MatrixGenerics_1.2.1 matrixStats_0.58.0 GenomicRanges_1.42.0
[17] GenomeInfoDb_1.26.7 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 splines_4.0.5
[6] gtools_3.8.2 blob_1.2.1 GenomeInfoDbData_1.2.4 pillar_1.6.1 RSQLite_2.2.7
[11] lattice_0.20-44 glue_1.4.2 digest_0.6.27 XVector_0.30.0 colorspace_2.0-1
[16] htmltools_0.5.1.1 Matrix_1.3-3 XML_3.99-0.6 pkgconfig_2.0.3 genefilter_1.72.1
[21] zlibbioc_1.36.0 purrr_0.3.4 xtable_1.8-4 scales_1.1.1 BiocParallel_1.24.1
[26] tibble_3.1.2 annotate_1.68.0 generics_0.1.0 farver_2.1.0 sjlabelled_1.1.8
[31] ellipsis_0.3.2 withr_2.4.2 survival_3.2-11 magrittr_2.0.1 crayon_1.4.1
[36] memoise_2.0.0 tools_4.0.5 lifecycle_1.0.0 munsell_0.5.0 locfit_1.5-9.4
[41] DelayedArray_0.16.3 AnnotationDbi_1.52.0 compiler_4.0.5 caTools_1.18.2 rlang_0.4.11
[46] grid_4.0.5 RCurl_1.98-1.3 dichromat_2.0-0 rstudioapi_0.13 htmlwidgets_1.5.3
[51] crosstalk_1.1.1 NOISeq_2.34.0 bitops_1.0-7 labeling_0.4.2 gtable_0.3.0
[56] DBI_1.1.1 R6_2.5.0 knitr_1.33 dplyr_1.0.6 bit_4.0.4
[61] insight_0.14.0 KernSmooth_2.23-20 Rcpp_1.0.6 vctrs_0.3.8 mapproj_1.2.7
[66] 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_D" "cop_D.1" "cop_D.2" "cop_L" "cop_L.1" "cop_L.2"
cop_D cop_D.1 cop_D.2 cop_L cop_L.1 cop_L.2
Pp3c1_20V3.1 253 200 237 389 389 378
Pp3c1_40V3.1 394 340 363 257 243 207
Pp3c1_60V3.1 574 456 525 475 525 521
Pp3c1_70V3.1 537 424 479 378 389 382
Pp3c1_80V3.1 11 5 9 2 3 0
Pp3c1_100V3.1 777 641 690 556 527 565
[1] "Raw data row number: 31315"
[1] "Raw data column number: 6"
[1] "Filtered data row number: 19859"
[1] "Filtered data row number: 6"
[1] "edgeR is running with cop_D vs. cop_L"
[1] "DESeq2 is running with cop_D vs. cop_L"
[1] "NOISeq is running with cop_D vs. cop_L"
Filtering out low count features...
19184 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_D" "cop_D.1" "cop_D.2" "cop_L" "cop_L.1" "cop_L.2"
[1] "cop_D"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-94.642 -24.696 -0.434 22.016 138.699
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 2.185e+02 4.174e+01 5.234 1.20e-06 ***
bx1 -1.279e+02 5.904e+01 -2.166 0.033115 *
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 -3.495e+06 5.622e+06 -0.622 0.535882
bx5 1.008e+03 1.574e+03 0.641 0.523479
bx6 -2.297e+02 1.200e+02 -1.915 0.058951 .
bx7 8.497e+01 5.317e+01 1.598 0.113760
bx8 1.643e+02 4.712e+01 3.488 0.000778 ***
bx9 2.044e+02 4.964e+01 4.119 8.88e-05 ***
bx10 1.321e+02 6.626e+01 1.993 0.049459 *
bx11 -1.321e+01 2.142e+02 -0.062 0.950996
bx12 -1.664e+02 1.248e+03 -0.133 0.894307
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 41.74 on 84 degrees of freedom
Multiple R-squared: 0.7347, Adjusted R-squared: 0.7031
F-statistic: 23.26 on 10 and 84 DF, p-value: < 2.2e-16
[1] "cop_D.1"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-84.84 -18.48 0.00 17.29 118.62
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 2.199e+02 3.572e+01 6.155 2.47e-08 ***
bx1 -1.405e+02 5.052e+01 -2.781 0.00669 **
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 -3.074e+06 4.811e+06 -0.639 0.52454
bx5 8.092e+02 1.347e+03 0.601 0.54950
bx6 -2.109e+02 1.027e+02 -2.054 0.04306 *
bx7 3.961e+01 4.550e+01 0.871 0.38649
bx8 1.119e+02 4.032e+01 2.776 0.00679 **
bx9 1.412e+02 4.248e+01 3.323 0.00132 **
bx10 8.138e+01 5.670e+01 1.435 0.15493
bx11 -1.450e+01 1.833e+02 -0.079 0.93713
bx12 -2.129e+02 1.068e+03 -0.199 0.84249
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 35.72 on 84 degrees of freedom
Multiple R-squared: 0.7219, Adjusted R-squared: 0.6888
F-statistic: 21.81 on 10 and 84 DF, p-value: < 2.2e-16
[1] "cop_D.2"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-89.91 -22.58 0.00 17.18 131.74
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 2.247e+02 3.903e+01 5.757 1.36e-07 ***
bx1 -1.427e+02 5.520e+01 -2.584 0.011495 *
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 -3.441e+06 5.257e+06 -0.655 0.514523
bx5 9.378e+02 1.471e+03 0.637 0.525640
bx6 -2.288e+02 1.122e+02 -2.039 0.044585 *
bx7 4.874e+01 4.972e+01 0.980 0.329734
bx8 1.299e+02 4.406e+01 2.949 0.004132 **
bx9 1.767e+02 4.642e+01 3.806 0.000268 ***
bx10 1.080e+02 6.196e+01 1.744 0.084896 .
bx11 -2.263e+01 2.003e+02 -0.113 0.910341
bx12 -6.157e+01 1.167e+03 -0.053 0.958066
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 39.03 on 84 degrees of freedom
Multiple R-squared: 0.7414, Adjusted R-squared: 0.7106
F-statistic: 24.08 on 10 and 84 DF, p-value: < 2.2e-16
[1] "cop_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-119.16 -26.25 0.00 21.17 159.68
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 2.308e+02 5.552e+01 4.157 7.73e-05 ***
bx1 -1.776e+02 7.852e+01 -2.262 0.02631 *
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 -3.953e+06 7.478e+06 -0.529 0.59849
bx5 1.135e+03 2.093e+03 0.542 0.58900
bx6 -2.564e+02 1.596e+02 -1.607 0.11182
bx7 9.949e+01 7.072e+01 1.407 0.16315
bx8 2.429e+02 6.267e+01 3.876 0.00021 ***
bx9 3.120e+02 6.603e+01 4.726 9.10e-06 ***
bx10 4.531e+02 8.813e+01 5.142 1.75e-06 ***
bx11 -1.656e+02 2.850e+02 -0.581 0.56283
bx12 -2.007e+02 1.661e+03 -0.121 0.90411
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 55.52 on 84 degrees of freedom
Multiple R-squared: 0.8115, Adjusted R-squared: 0.789
F-statistic: 36.15 on 10 and 84 DF, p-value: < 2.2e-16
[1] "cop_L.1"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-123.160 -26.519 -0.303 23.664 170.626
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 2.598e+02 5.740e+01 4.526 1.96e-05 ***
bx1 -2.058e+02 8.117e+01 -2.536 0.01308 *
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 -4.172e+06 7.730e+06 -0.540 0.59087
bx5 1.187e+03 2.164e+03 0.549 0.58464
bx6 -2.919e+02 1.650e+02 -1.769 0.08044 .
bx7 8.117e+01 7.310e+01 1.110 0.27002
bx8 2.198e+02 6.479e+01 3.393 0.00106 **
bx9 3.022e+02 6.825e+01 4.428 2.84e-05 ***
bx10 4.652e+02 9.110e+01 5.107 2.01e-06 ***
bx11 -1.266e+02 2.946e+02 -0.430 0.66836
bx12 -2.734e+02 1.717e+03 -0.159 0.87382
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 57.4 on 84 degrees of freedom
Multiple R-squared: 0.8145, Adjusted R-squared: 0.7924
F-statistic: 36.88 on 10 and 84 DF, p-value: < 2.2e-16
[1] "cop_L.2"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-120.33 -28.27 0.00 22.42 166.78
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 2.606e+02 5.637e+01 4.622 1.36e-05 ***
bx1 -2.079e+02 7.972e+01 -2.608 0.01077 *
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 -4.177e+06 7.592e+06 -0.550 0.58368
bx5 1.198e+03 2.125e+03 0.564 0.57445
bx6 -3.024e+02 1.620e+02 -1.867 0.06543 .
bx7 7.848e+01 7.180e+01 1.093 0.27746
bx8 2.162e+02 6.363e+01 3.398 0.00104 **
bx9 2.896e+02 6.703e+01 4.320 4.25e-05 ***
bx10 4.513e+02 8.948e+01 5.044 2.59e-06 ***
bx11 -1.181e+02 2.893e+02 -0.408 0.68406
bx12 -2.645e+02 1.686e+03 -0.157 0.87571
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 56.37 on 84 degrees of freedom
Multiple R-squared: 0.8141, Adjusted R-squared: 0.7919
F-statistic: 36.78 on 10 and 84 DF, p-value: < 2.2e-16
[1] "GC content bias detection is to be computed for:"
[1] "cop_D" "cop_L"
[1] "cop_D"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-11.786 -2.889 0.000 2.437 17.090
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 2.898e+01 5.091e+00 5.693 1.79e-07 ***
bx1 -1.799e+01 7.200e+00 -2.499 0.014413 *
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 -4.362e+05 6.857e+05 -0.636 0.526427
bx5 1.197e+02 1.919e+02 0.624 0.534418
bx6 -2.918e+01 1.463e+01 -1.994 0.049379 *
bx7 7.443e+00 6.484e+00 1.148 0.254310
bx8 1.762e+01 5.747e+00 3.067 0.002911 **
bx9 2.269e+01 6.054e+00 3.748 0.000327 ***
bx10 1.398e+01 8.081e+00 1.730 0.087261 .
bx11 -2.367e+00 2.613e+01 -0.091 0.928024
bx12 -1.883e+01 1.523e+02 -0.124 0.901897
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 5.091 on 84 degrees of freedom
Multiple R-squared: 0.7319, Adjusted R-squared: 0.6999
F-statistic: 22.93 on 10 and 84 DF, p-value: < 2.2e-16
[1] "cop_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-12.040 -2.697 0.000 2.239 16.532
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 2.498e+01 5.617e+00 4.448 2.64e-05 ***
bx1 -1.966e+01 7.944e+00 -2.475 0.015350 *
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 -4.079e+05 7.565e+05 -0.539 0.591201
bx5 1.167e+02 2.117e+02 0.551 0.583124
bx6 -2.829e+01 1.614e+01 -1.752 0.083400 .
bx7 8.542e+00 7.154e+00 1.194 0.235841
bx8 2.247e+01 6.340e+00 3.545 0.000645 ***
bx9 2.996e+01 6.679e+00 4.485 2.29e-05 ***
bx10 4.534e+01 8.915e+00 5.085 2.20e-06 ***
bx11 -1.360e+01 2.883e+01 -0.472 0.638346
bx12 -2.500e+01 1.680e+02 -0.149 0.882030
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 5.617 on 84 degrees of freedom
Multiple R-squared: 0.8132, Adjusted R-squared: 0.791
F-statistic: 36.57 on 10 and 84 DF, p-value: < 2.2e-16
[1] "cop_D"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-11.786 -2.889 0.000 2.437 17.090
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 2.898e+01 5.091e+00 5.693 1.79e-07 ***
bx1 -1.799e+01 7.200e+00 -2.499 0.014413 *
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 -4.362e+05 6.857e+05 -0.636 0.526427
bx5 1.197e+02 1.919e+02 0.624 0.534418
bx6 -2.918e+01 1.463e+01 -1.994 0.049379 *
bx7 7.443e+00 6.484e+00 1.148 0.254310
bx8 1.762e+01 5.747e+00 3.067 0.002911 **
bx9 2.269e+01 6.054e+00 3.748 0.000327 ***
bx10 1.398e+01 8.081e+00 1.730 0.087261 .
bx11 -2.367e+00 2.613e+01 -0.091 0.928024
bx12 -1.883e+01 1.523e+02 -0.124 0.901897
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 5.091 on 84 degrees of freedom
Multiple R-squared: 0.7319, Adjusted R-squared: 0.6999
F-statistic: 22.93 on 10 and 84 DF, p-value: < 2.2e-16
[1] "cop_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-12.040 -2.697 0.000 2.239 16.532
Coefficients: (3 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 2.498e+01 5.617e+00 4.448 2.64e-05 ***
bx1 -1.966e+01 7.944e+00 -2.475 0.015350 *
bx2 NA NA NA NA
bx3 NA NA NA NA
bx4 -4.079e+05 7.565e+05 -0.539 0.591201
bx5 1.167e+02 2.117e+02 0.551 0.583124
bx6 -2.829e+01 1.614e+01 -1.752 0.083400 .
bx7 8.542e+00 7.154e+00 1.194 0.235841
bx8 2.247e+01 6.340e+00 3.545 0.000645 ***
bx9 2.996e+01 6.679e+00 4.485 2.29e-05 ***
bx10 4.534e+01 8.915e+00 5.085 2.20e-06 ***
bx11 -1.360e+01 2.883e+01 -0.472 0.638346
bx12 -2.500e+01 1.680e+02 -0.149 0.882030
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 5.617 on 84 degrees of freedom
Multiple R-squared: 0.8132, Adjusted R-squared: 0.791
F-statistic: 36.57 on 10 and 84 DF, p-value: < 2.2e-16
[1] "Length bias detection information is to be computed for:"
[1] "cop_D" "cop_D.1" "cop_D.2" "cop_L" "cop_L.1" "cop_L.2"
[1] "cop_D"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-59.184 -17.186 -2.937 16.606 86.362
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 1152.65 28.65 40.236 <2e-16 ***
bx1 -1104.29 40.16 -27.496 <2e-16 ***
bx2 -1110.47 44.05 -25.212 <2e-16 ***
bx3 -828.59 37.09 -22.340 <2e-16 ***
bx4 -931.94 32.78 -28.427 <2e-16 ***
bx5 -807.55 32.41 -24.917 <2e-16 ***
bx6 -769.86 33.62 -22.899 <2e-16 ***
bx7 -738.48 36.70 -20.123 <2e-16 ***
bx8 -583.24 43.93 -13.277 <2e-16 ***
bx9 -699.45 66.54 -10.511 <2e-16 ***
bx10 -125.49 176.27 -0.712 0.4785
bx11 -6138.06 3281.12 -1.871 0.0650 .
bx12 113861.90 62153.35 1.832 0.0706 .
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 28.65 on 82 degrees of freedom
Multiple R-squared: 0.9652, Adjusted R-squared: 0.9601
F-statistic: 189.5 on 12 and 82 DF, p-value: < 2.2e-16
[1] "cop_D.1"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-53.638 -16.739 -1.086 16.417 75.970
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 885.44 25.19 35.145 < 2e-16 ***
bx1 -840.51 35.32 -23.796 < 2e-16 ***
bx2 -839.46 38.74 -21.671 < 2e-16 ***
bx3 -580.59 32.62 -17.799 < 2e-16 ***
bx4 -688.94 28.83 -23.895 < 2e-16 ***
bx5 -583.48 28.50 -20.470 < 2e-16 ***
bx6 -564.56 29.57 -19.094 < 2e-16 ***
bx7 -537.96 32.27 -16.668 < 2e-16 ***
bx8 -408.17 38.63 -10.565 < 2e-16 ***
bx9 -532.31 58.52 -9.096 4.64e-14 ***
bx10 -15.54 155.02 -0.100 0.9204
bx11 -5607.73 2885.65 -1.943 0.0554 .
bx12 104479.45 54661.97 1.911 0.0595 .
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 25.19 on 82 degrees of freedom
Multiple R-squared: 0.9526, Adjusted R-squared: 0.9457
F-statistic: 137.4 on 12 and 82 DF, p-value: < 2.2e-16
[1] "cop_D.2"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-55.677 -18.355 -2.962 14.906 81.700
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 1023.56 27.44 37.299 < 2e-16 ***
bx1 -978.65 38.47 -25.437 < 2e-16 ***
bx2 -984.71 42.19 -23.338 < 2e-16 ***
bx3 -702.30 35.53 -19.767 < 2e-16 ***
bx4 -821.07 31.40 -26.145 < 2e-16 ***
bx5 -701.34 31.05 -22.590 < 2e-16 ***
bx6 -668.61 32.21 -20.761 < 2e-16 ***
bx7 -640.97 35.16 -18.233 < 2e-16 ***
bx8 -507.39 42.08 -12.057 < 2e-16 ***
bx9 -600.41 63.75 -9.419 1.06e-14 ***
bx10 -120.49 168.86 -0.714 0.478
bx11 -4818.55 3143.16 -1.533 0.129
bx12 87808.84 59539.86 1.475 0.144
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 27.44 on 82 degrees of freedom
Multiple R-squared: 0.959, Adjusted R-squared: 0.953
F-statistic: 159.9 on 12 and 82 DF, p-value: < 2.2e-16
[1] "cop_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-89.425 -29.640 -1.392 30.877 129.921
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 815.380 45.146 18.061 < 2e-16 ***
bx1 -775.426 63.294 -12.251 < 2e-16 ***
bx2 -765.901 69.413 -11.034 < 2e-16 ***
bx3 -267.708 58.451 -4.580 1.64e-05 ***
bx4 -464.790 51.665 -8.996 7.32e-14 ***
bx5 -343.702 51.077 -6.729 2.14e-09 ***
bx6 -423.639 52.983 -7.996 7.12e-12 ***
bx7 -356.958 57.834 -6.172 2.45e-08 ***
bx8 -319.030 69.231 -4.608 1.47e-05 ***
bx9 -369.680 104.869 -3.525 0.000696 ***
bx10 -5.511 277.792 -0.020 0.984220
bx11 -4557.522 5170.890 -0.881 0.380688
bx12 86068.622 97950.596 0.879 0.382135
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 45.15 on 82 degrees of freedom
Multiple R-squared: 0.7845, Adjusted R-squared: 0.753
F-statistic: 24.88 on 12 and 82 DF, p-value: < 2.2e-16
[1] "cop_L.1"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-83.017 -31.359 -1.711 28.571 142.286
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 802.79 47.10 17.043 < 2e-16 ***
bx1 -760.76 66.04 -11.520 < 2e-16 ***
bx2 -760.88 72.42 -10.506 < 2e-16 ***
bx3 -209.07 60.98 -3.428 0.000953 ***
bx4 -440.55 53.90 -8.173 3.18e-12 ***
bx5 -316.39 53.29 -5.937 6.70e-08 ***
bx6 -407.59 55.28 -7.373 1.20e-10 ***
bx7 -338.90 60.34 -5.616 2.59e-07 ***
bx8 -307.00 72.23 -4.250 5.61e-05 ***
bx9 -365.20 109.41 -3.338 0.001272 **
bx10 14.90 289.83 0.051 0.959133
bx11 -4682.76 5395.03 -0.868 0.387941
bx12 88334.10 102196.36 0.864 0.389913
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 47.1 on 82 degrees of freedom
Multiple R-squared: 0.7603, Adjusted R-squared: 0.7252
F-statistic: 21.67 on 12 and 82 DF, p-value: < 2.2e-16
[1] "cop_L.2"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-84.290 -31.614 -1.432 28.806 138.012
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 838.47 45.26 18.525 < 2e-16 ***
bx1 -796.96 63.45 -12.560 < 2e-16 ***
bx2 -798.01 69.59 -11.467 < 2e-16 ***
bx3 -284.50 58.60 -4.855 5.67e-06 ***
bx4 -478.53 51.80 -9.239 2.41e-14 ***
bx5 -362.07 51.21 -7.071 4.68e-10 ***
bx6 -438.90 53.12 -8.263 2.10e-12 ***
bx7 -373.09 57.98 -6.435 7.81e-09 ***
bx8 -335.32 69.41 -4.831 6.23e-06 ***
bx9 -376.14 105.14 -3.578 0.000585 ***
bx10 -44.95 278.50 -0.161 0.872182
bx11 -3796.69 5184.03 -0.732 0.466024
bx12 70584.20 98199.56 0.719 0.474318
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 45.26 on 82 degrees of freedom
Multiple R-squared: 0.7941, Adjusted R-squared: 0.764
F-statistic: 26.35 on 12 and 82 DF, p-value: < 2.2e-16
[1] "Length bias detection information is to be computed for:"
[1] "cop_D" "cop_L"
[1] "cop_D"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-7.2896 -2.3985 -0.4766 2.0865 10.6075
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 133.026 3.529 37.694 < 2e-16 ***
bx1 -126.994 4.948 -25.667 < 2e-16 ***
bx2 -127.467 5.426 -23.491 < 2e-16 ***
bx3 -91.528 4.569 -20.031 < 2e-16 ***
bx4 -106.022 4.039 -26.251 < 2e-16 ***
bx5 -90.786 3.993 -22.738 < 2e-16 ***
bx6 -86.925 4.142 -20.988 < 2e-16 ***
bx7 -83.214 4.521 -18.406 < 2e-16 ***
bx8 -64.939 5.412 -11.999 < 2e-16 ***
bx9 -79.638 8.198 -9.715 2.74e-15 ***
bx10 -10.671 21.715 -0.491 0.6245
bx11 -728.089 404.216 -1.801 0.0753 .
bx12 13457.307 7656.934 1.758 0.0826 .
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 3.529 on 82 degrees of freedom
Multiple R-squared: 0.9597, Adjusted R-squared: 0.9538
F-statistic: 162.8 on 12 and 82 DF, p-value: < 2.2e-16
[1] "cop_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-8.2709 -3.1320 -0.1445 2.8974 13.6042
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 81.537 4.559 17.886 < 2e-16 ***
bx1 -77.438 6.391 -12.116 < 2e-16 ***
bx2 -77.177 7.009 -11.011 < 2e-16 ***
bx3 -25.277 5.902 -4.283 4.99e-05 ***
bx4 -45.934 5.217 -8.804 1.76e-13 ***
bx5 -33.941 5.158 -6.581 4.12e-09 ***
bx6 -42.153 5.350 -7.879 1.21e-11 ***
bx7 -35.475 5.840 -6.074 3.72e-08 ***
bx8 -31.921 6.991 -4.566 1.73e-05 ***
bx9 -36.841 10.590 -3.479 0.000809 ***
bx10 -1.299 28.051 -0.046 0.963187
bx11 -430.739 522.152 -0.825 0.411805
bx12 8094.888 9890.966 0.818 0.415494
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 4.559 on 82 degrees of freedom
Multiple R-squared: 0.7799, Adjusted R-squared: 0.7477
F-statistic: 24.21 on 12 and 82 DF, p-value: < 2.2e-16
[1] "cop_D"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-7.2896 -2.3985 -0.4766 2.0865 10.6075
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 133.026 3.529 37.694 < 2e-16 ***
bx1 -126.994 4.948 -25.667 < 2e-16 ***
bx2 -127.467 5.426 -23.491 < 2e-16 ***
bx3 -91.528 4.569 -20.031 < 2e-16 ***
bx4 -106.022 4.039 -26.251 < 2e-16 ***
bx5 -90.786 3.993 -22.738 < 2e-16 ***
bx6 -86.925 4.142 -20.988 < 2e-16 ***
bx7 -83.214 4.521 -18.406 < 2e-16 ***
bx8 -64.939 5.412 -11.999 < 2e-16 ***
bx9 -79.638 8.198 -9.715 2.74e-15 ***
bx10 -10.671 21.715 -0.491 0.6245
bx11 -728.089 404.216 -1.801 0.0753 .
bx12 13457.307 7656.934 1.758 0.0826 .
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 3.529 on 82 degrees of freedom
Multiple R-squared: 0.9597, Adjusted R-squared: 0.9538
F-statistic: 162.8 on 12 and 82 DF, p-value: < 2.2e-16
[1] "cop_L"
Call:
lm(formula = datos[, i] ~ bx)
Residuals:
Min 1Q Median 3Q Max
-8.2709 -3.1320 -0.1445 2.8974 13.6042
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 81.537 4.559 17.886 < 2e-16 ***
bx1 -77.438 6.391 -12.116 < 2e-16 ***
bx2 -77.177 7.009 -11.011 < 2e-16 ***
bx3 -25.277 5.902 -4.283 4.99e-05 ***
bx4 -45.934 5.217 -8.804 1.76e-13 ***
bx5 -33.941 5.158 -6.581 4.12e-09 ***
bx6 -42.153 5.350 -7.879 1.21e-11 ***
bx7 -35.475 5.840 -6.074 3.72e-08 ***
bx8 -31.921 6.991 -4.566 1.73e-05 ***
bx9 -36.841 10.590 -3.479 0.000809 ***
bx10 -1.299 28.051 -0.046 0.963187
bx11 -430.739 522.152 -0.825 0.411805
bx12 8094.888 9890.966 0.818 0.415494
bx13 NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 4.559 on 82 degrees of freedom
Multiple R-squared: 0.7799, Adjusted R-squared: 0.7477
F-statistic: 24.21 on 12 and 82 DF, p-value: < 2.2e-16
[1] "Reference sample is: cop_D"
[1] "Confidence intervals for median of M:"
0.5% 99.5% Diagnostic Test
cop_D.1 "-0.031989841848585" "-0.0202078338192909" "FAILED"
cop_D.2 "0.00213357203682632" "0.0105379483014003" "FAILED"
cop_L "-0.129716094307598" "-0.0698509563783147" "FAILED"
cop_L.1 "-0.146083574696735" "-0.0844714918104378" "FAILED"
cop_L.2 "-0.122647071729454" "-0.0659655625249422" "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...
18510 features are to be kept for differential expression analysis with filtering method 1
...k-means clustering done
Size of 15 clusters:
[1] 166 234 545 1748 49 15 14 672 11083 2 33 7 79 3751 112
Resampling cluster...[1] 1
[1] 2
[1] 3
[1] 4
Size of 15 subclusters of cluster: 4
[1] 209 112 169 153 73 89 173 160 90 80 92 111 111 55 71
[1] 5
[1] 6
[1] 7
[1] 8
[1] 9
Size of 15 subclusters of cluster: 9
[1] 1871 441 588 360 858 448 666 596 924 596 286 1048 574 691 1136
[1] 10
[1] 11
[1] 12
[1] 13
[1] 14
Size of 15 subclusters of cluster: 14
[1] 320 225 133 89 198 187 343 529 172 206 142 146 453 325 283
[1] 15
Computing Z for noise...
Computing probability of differential expression...
p0 = 0.0802683495922669
Probability
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.9602 0.9975 0.9182 1.0000 1.0000 674
Computing Z values...
Filtering out low count features...
19184 features are to be kept for differential expression analysis with filtering method 1
...k-means clustering done
Size of 15 clusters:
[1] 567 4955 165 7 10531 2 1544 225 49 46 16 148 836 78 15
Resampling cluster...[1] 1
[1] 2
Size of 15 subclusters of cluster: 2
[1] 228 458 327 418 132 640 148 145 339 446 511 299 320 214 330
[1] 3
[1] 4
[1] 5
Size of 15 subclusters of cluster: 5
[1] 229 266 2196 1077 926 412 641 831 548 693 404 389 523 781 615
[1] 6
[1] 7
Size of 15 subclusters of cluster: 7
[1] 62 133 50 181 141 73 73 94 64 155 96 126 91 103 102
[1] 8
[1] 9
[1] 10
[1] 11
[1] 12
[1] 13
[1] 14
[1] 15
Computing Z for noise...
Computing probability of differential expression...
p0 = 0.0913900850194875
Probability
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.0000 0.9428 0.9962 0.9064 1.0000 1.0000
Computing Z values...
Filtering out low count features...
19184 features are to be kept for differential expression analysis with filtering method 1
...k-means clustering done
Size of 15 clusters:
[1] 14 3 1676 89 8196 87 36 457 1871 5350 40 120 901 11 333
Resampling cluster...[1] 1
[1] 2
[1] 3
Size of 15 subclusters of cluster: 3
[1] 79 159 154 42 90 83 173 98 134 74 206 111 95 119 59
[1] 4
[1] 5
Size of 15 subclusters of cluster: 5
[1] 452 422 613 748 193 268 315 337 612 468 286 407 497 2178 400
[1] 6
[1] 7
[1] 8
[1] 9
Size of 15 subclusters of cluster: 9
[1] 89 189 65 138 157 126 183 113 124 81 94 170 92 90 160
[1] 10
Size of 15 subclusters of cluster: 10
[1] 256 413 156 402 445 303 585 362 313 503 331 386 228 245 422
[1] 11
[1] 12
[1] 13
[1] 14
[1] 15
Computing Z for noise...
Computing probability of differential expression...
p0 = 0.0945897344082129
Probability
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.0000 0.9389 0.9962 0.9008 1.0000 1.0000
[1] "10391 differentially expressed features"
[1] "5388 differentially expressed features (up in first condition)"
[1] "5003 differentially expressed features (down in first condition)"
[1] "10196 differentially expressed features"
[1] "3540 differentially expressed features (up in first condition)"
[1] "6656 differentially expressed features (down in first condition)"
[1] "8635 differentially expressed features"
[1] "11729 differentially expressed features"
[1] "8216 differentially expressed features"
[1] "10927 differentially expressed features"
[1] "8602 differentially expressed features"
[1] "11649 differentially expressed features"
[1] "15316 differentially expressed features"
[1] "10391 differentially expressed features"
[1] "15244 differentially expressed features"
[1] "10196 differentially expressed features"
[1] "8635 differentially expressed features"
[1] "8216 differentially expressed features"
[1] "DEGs edgeR"
[1] 14109
[1] "DEGs deseq2"
[1] 12443
[1] "DEGs noiseq"
[1] 8635
[1] "DEGs noiseqbio"
[1] 10391
[1] "DEGs intersection without direction check (four methods)"
[1] 8440
[1] "Pp3c1_40V3.1" "Pp3c1_70V3.1" "Pp3c1_100V3.1" "Pp3c1_200V3.1" "Pp3c1_370V3.1" "Pp3c1_400V3.1" "Pp3c1_470V3.1"
[8] "Pp3c1_540V3.1" "Pp3c1_580V3.1" "Pp3c1_620V3.1" "Pp3c1_680V3.1" "Pp3c1_690V3.1" "Pp3c1_890V3.1" "Pp3c1_900V3.1"
[15] "Pp3c1_950V3.1" "Pp3c1_1000V3.1" "Pp3c1_1160V3.1" "Pp3c1_1240V3.1" "Pp3c1_1260V3.1" "Pp3c1_1330V3.1" "Pp3c1_1390V3.1"
[22] "Pp3c1_1570V3.1" "Pp3c1_1650V3.1" "Pp3c1_1790V3.1" "Pp3c1_1800V3.1" "Pp3c1_1810V3.1" "Pp3c1_1860V3.1" "Pp3c1_1870V3.1"
[29] "Pp3c1_1940V3.1" "Pp3c1_2010V3.1" "Pp3c1_2170V3.1" "Pp3c1_2210V3.1" "Pp3c1_2220V3.1" "Pp3c1_2420V3.1" "Pp3c1_2540V3.1"
[36] "Pp3c1_2740V3.1" "Pp3c1_2920V3.1" "Pp3c1_2980V3.1" "Pp3c1_3000V3.1" "Pp3c1_3040V3.1" "Pp3c1_3140V3.1" "Pp3c1_3160V3.1"
[43] "Pp3c1_3180V3.1" "Pp3c1_3200V3.1" "Pp3c1_3210V3.1" "Pp3c1_3220V3.1" "Pp3c1_3230V3.1" "Pp3c1_3260V3.1" "Pp3c1_3300V3.1"
[50] "Pp3c1_3440V3.1" "Pp3c1_3500V3.1" "Pp3c1_3590V3.1" "Pp3c1_3610V3.1" "Pp3c1_3700V3.1" "Pp3c1_3730V3.1" "Pp3c1_3750V3.1"
[57] "Pp3c1_3890V3.1" "Pp3c1_4010V3.1" "Pp3c1_4030V3.1" "Pp3c1_4050V3.1" "Pp3c1_4120V3.1" "Pp3c1_4140V3.1" "Pp3c1_4180V3.1"
[64] "Pp3c1_4270V3.1" "Pp3c1_4350V3.1" "Pp3c1_4400V3.1" "Pp3c1_4470V3.1" "Pp3c1_4510V3.1" "Pp3c1_4540V3.1" "Pp3c1_4600V3.1"
[71] "Pp3c1_4750V3.1" "Pp3c1_4990V3.1" "Pp3c1_5050V3.1" "Pp3c1_5280V3.1" "Pp3c1_5300V3.1" "Pp3c1_5320V3.1" "Pp3c1_5460V3.1"
[78] "Pp3c1_5570V3.1" "Pp3c1_5800V3.1" "Pp3c1_5820V3.1" "Pp3c1_5850V3.1" "Pp3c1_5870V3.1" "Pp3c1_6020V3.1" "Pp3c1_6050V3.1"
[85] "Pp3c1_6090V3.1" "Pp3c1_6110V3.1" "Pp3c1_6130V3.1" "Pp3c1_6280V3.1" "Pp3c1_6360V3.1" "Pp3c1_6380V3.1" "Pp3c1_6450V3.1"
[92] "Pp3c1_6470V3.1" "Pp3c1_6480V3.1" "Pp3c1_6500V3.1" "Pp3c1_6570V3.1" "Pp3c1_6750V3.1" "Pp3c1_6930V3.1" "Pp3c1_6950V3.1"
[99] "Pp3c1_7010V3.1" "Pp3c1_7030V3.1" "Pp3c1_7090V3.1" "Pp3c1_7160V3.1" "Pp3c1_7220V3.1" "Pp3c1_7300V3.1" "Pp3c1_7360V3.1"
[106] "Pp3c1_7370V3.1" "Pp3c1_7380V3.1" "Pp3c1_7390V3.1" "Pp3c1_7450V3.1" "Pp3c1_7500V3.1" "Pp3c1_7520V3.1" "Pp3c1_7540V3.1"
[113] "Pp3c1_7590V3.1" "Pp3c1_7710V3.1" "Pp3c1_7720V3.1" "Pp3c1_7800V3.1" "Pp3c1_7810V3.1" "Pp3c1_7830V3.1" "Pp3c1_7880V3.1"
[120] "Pp3c1_7950V3.1" "Pp3c1_8060V3.1" "Pp3c1_8080V3.1" "Pp3c1_8110V3.1" "Pp3c1_8170V3.1" "Pp3c1_8190V3.1" "Pp3c1_8210V3.1"
[127] "Pp3c1_8240V3.1" "Pp3c1_8280V3.1" "Pp3c1_8450V3.1" "Pp3c1_8490V3.1" "Pp3c1_8530V3.1" "Pp3c1_8870V3.1" "Pp3c1_8890V3.1"
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[148] "Pp3c1_10220V3.1" "Pp3c1_10400V3.1" "Pp3c1_10470V3.1" "Pp3c1_10530V3.1" "Pp3c1_10540V3.1" "Pp3c1_10570V3.1" "Pp3c1_10620V3.1"
[155] "Pp3c1_10630V3.1" "Pp3c1_10810V3.1" "Pp3c1_10880V3.1" "Pp3c1_10970V3.1" "Pp3c1_11030V3.1" "Pp3c1_11050V3.1" "Pp3c1_11090V3.1"
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[176] "Pp3c1_12860V3.1" "Pp3c1_12940V3.1" "Pp3c1_13120V3.1" "Pp3c1_13170V3.1" "Pp3c1_13270V3.1" "Pp3c1_13308V3.1" "Pp3c1_13430V3.1"
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[197] "Pp3c1_14760V3.1" "Pp3c1_14770V3.1" "Pp3c1_14800V3.1" "Pp3c1_14870V3.1" "Pp3c1_14910V3.1" "Pp3c1_14920V3.1" "Pp3c1_14980V3.1"
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[211] "Pp3c1_15400V3.1" "Pp3c1_15410V3.1" "Pp3c1_15460V3.1" "Pp3c1_15560V3.1" "Pp3c1_15690V3.1" "Pp3c1_15730V3.1" "Pp3c1_15750V3.1"
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[225] "Pp3c1_16850V3.1" "Pp3c1_16900V3.1" "Pp3c1_16980V3.1" "Pp3c1_17080V3.1" "Pp3c1_17220V3.1" "Pp3c1_17710V3.1" "Pp3c1_17860V3.1"
[232] "Pp3c1_18050V3.1" "Pp3c1_18130V3.1" "Pp3c1_18150V3.1" "Pp3c1_18250V3.1" "Pp3c1_18260V3.1" "Pp3c1_18440V3.1" "Pp3c1_18460V3.1"
[239] "Pp3c1_18530V3.1" "Pp3c1_18680V3.1" "Pp3c1_18830V3.1" "Pp3c1_18860V3.1" "Pp3c1_18910V3.1" "Pp3c1_18940V3.1" "Pp3c1_19060V3.1"
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[253] "Pp3c1_19400V3.1" "Pp3c1_19660V3.1" "Pp3c1_19950V3.1" "Pp3c1_20280V3.1" "Pp3c1_20310V3.1" "Pp3c1_20350V3.1" "Pp3c1_20430V3.1"
[260] "Pp3c1_20630V3.1" "Pp3c1_20640V3.1" "Pp3c1_20690V3.1" "Pp3c1_20700V3.1" "Pp3c1_20710V3.1" "Pp3c1_20753V3.1" "Pp3c1_20770V3.1"
[267] "Pp3c1_20790V3.1" "Pp3c1_20810V3.1" "Pp3c1_20870V3.1" "Pp3c1_20880V3.1" "Pp3c1_20960V3.1" "Pp3c1_20980V3.1" "Pp3c1_21110V3.1"
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[281] "Pp3c1_21540V3.1" "Pp3c1_21550V3.1" "Pp3c1_21620V3.1" "Pp3c1_21630V3.1" "Pp3c1_21650V3.1" "Pp3c1_21730V3.1" "Pp3c1_21760V3.1"
[288] "Pp3c1_21810V3.1" "Pp3c1_21850V3.1" "Pp3c1_21890V3.1" "Pp3c1_21920V3.1" "Pp3c1_22040V3.1" "Pp3c1_22090V3.1" "Pp3c1_22120V3.1"
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[652] "Pp3c2_5490V3.1" "Pp3c2_5520V3.1" "Pp3c2_5530V3.1" "Pp3c2_5560V3.1" "Pp3c2_5625V3.1" "Pp3c2_5780V3.1" "Pp3c2_5910V3.1"
[659] "Pp3c2_5960V3.1" "Pp3c2_5990V3.1" "Pp3c2_6040V3.1" "Pp3c2_6080V3.1" "Pp3c2_6132V3.1" "Pp3c2_6160V3.1" "Pp3c2_6200V3.1"
[666] "Pp3c2_6220V3.1" "Pp3c2_6240V3.1" "Pp3c2_6370V3.1" "Pp3c2_6520V3.1" "Pp3c2_6560V3.1" "Pp3c2_6630V3.1" "Pp3c2_6650V3.1"
[673] "Pp3c2_6690V3.1" "Pp3c2_6730V3.1" "Pp3c2_6740V3.1" "Pp3c2_6750V3.1" "Pp3c2_6770V3.1" "Pp3c2_6800V3.1" "Pp3c2_7230V3.1"
[680] "Pp3c2_7620V3.1" "Pp3c2_7760V3.1" "Pp3c2_7790V3.1" "Pp3c2_7910V3.1" "Pp3c2_7940V3.1" "Pp3c2_8099V3.1" "Pp3c2_8340V3.1"
[687] "Pp3c2_8360V3.1" "Pp3c2_8410V3.1" "Pp3c2_8420V3.1" "Pp3c2_8470V3.1" "Pp3c2_8570V3.1" "Pp3c2_8610V3.1" "Pp3c2_8660V3.1"
[694] "Pp3c2_8770V3.1" "Pp3c2_8820V3.1" "Pp3c2_8880V3.1" "Pp3c2_8960V3.1" "Pp3c2_9020V3.1" "Pp3c2_9080V3.1" "Pp3c2_9140V3.1"
[701] "Pp3c2_9150V3.1" "Pp3c2_9310V3.1" "Pp3c2_9460V3.1" "Pp3c2_9470V3.1" "Pp3c2_9480V3.1" "Pp3c2_9490V3.1" "Pp3c2_9610V3.1"
[708] "Pp3c2_9630V3.1" "Pp3c2_9813V3.1" "Pp3c2_9820V3.1" "Pp3c2_9830V3.1" "Pp3c2_9850V3.1" "Pp3c2_9870V3.1" "Pp3c2_9920V3.1"
[715] "Pp3c2_9940V3.1" "Pp3c2_10070V3.1" "Pp3c2_10260V3.1" "Pp3c2_10280V3.1" "Pp3c2_10310V3.1" "Pp3c2_10530V3.1" "Pp3c2_10610V3.1"
[722] "Pp3c2_10630V3.1" "Pp3c2_10900V3.1" "Pp3c2_10920V3.1" "Pp3c2_11030V3.1" "Pp3c2_11130V3.1" "Pp3c2_11190V3.1" "Pp3c2_11210V3.1"
[729] "Pp3c2_11250V3.1" "Pp3c2_11370V3.1" "Pp3c2_11380V3.1" "Pp3c2_11410V3.1" "Pp3c2_11490V3.1" "Pp3c2_11580V3.1" "Pp3c2_11670V3.1"
[736] "Pp3c2_11730V3.1" "Pp3c2_11820V3.1" "Pp3c2_11870V3.1" "Pp3c2_11890V3.1" "Pp3c2_12080V3.1" "Pp3c2_12120V3.1" "Pp3c2_12150V3.1"
[743] "Pp3c2_12240V3.1" "Pp3c2_12290V3.1" "Pp3c2_12370V3.1" "Pp3c2_12550V3.1" "Pp3c2_12620V3.1" "Pp3c2_12640V3.1" "Pp3c2_12670V3.1"
[750] "Pp3c2_12680V3.1" "Pp3c2_13250V3.1" "Pp3c2_13270V3.1" "Pp3c2_13280V3.1" "Pp3c2_13290V3.1" "Pp3c2_13330V3.1" "Pp3c2_13400V3.1"
[757] "Pp3c2_13410V3.1" "Pp3c2_13420V3.1" "Pp3c2_13450V3.1" "Pp3c2_13560V3.1" "Pp3c2_13590V3.1" "Pp3c2_13670V3.1" "Pp3c2_13790V3.1"
[764] "Pp3c2_13820V3.1" "Pp3c2_13870V3.1" "Pp3c2_13880V3.1" "Pp3c2_13930V3.1" "Pp3c2_13970V3.1" "Pp3c2_14060V3.1" "Pp3c2_14090V3.1"
[771] "Pp3c2_14120V3.1" "Pp3c2_14270V3.1" "Pp3c2_14290V3.1" "Pp3c2_14350V3.1" "Pp3c2_14400V3.1" "Pp3c2_14410V3.1" "Pp3c2_14470V3.1"
[778] "Pp3c2_14520V3.1" "Pp3c2_14560V3.1" "Pp3c2_14570V3.1" "Pp3c2_14600V3.1" "Pp3c2_14610V3.1" "Pp3c2_14800V3.1" "Pp3c2_14820V3.1"
[785] "Pp3c2_14930V3.1" "Pp3c2_15060V3.1" "Pp3c2_15140V3.1" "Pp3c2_15180V3.1" "Pp3c2_15200V3.1" "Pp3c2_15250V3.1" "Pp3c2_15400V3.1"
[792] "Pp3c2_15430V3.1" "Pp3c2_15480V3.1" "Pp3c2_15490V3.1" "Pp3c2_15500V3.1" "Pp3c2_15510V3.1" "Pp3c2_15820V3.1" "Pp3c2_15900V3.1"
[799] "Pp3c2_15910V3.1" "Pp3c2_15950V3.1" "Pp3c2_16030V3.1" "Pp3c2_16160V3.1" "Pp3c2_16250V3.1" "Pp3c2_16300V3.1" "Pp3c2_16310V3.1"
[806] "Pp3c2_16610V3.1" "Pp3c2_16660V3.1" "Pp3c2_16770V3.1" "Pp3c2_16800V3.1" "Pp3c2_16830V3.1" "Pp3c2_17000V3.1" "Pp3c2_17040V3.1"
[813] "Pp3c2_17110V3.1" "Pp3c2_17140V3.1" "Pp3c2_17270V3.1" "Pp3c2_17290V3.1" "Pp3c2_17370V3.1" "Pp3c2_17380V3.1" "Pp3c2_17390V3.1"
[820] "Pp3c2_17450V3.1" "Pp3c2_17510V3.1" "Pp3c2_17540V3.1" "Pp3c2_17560V3.1" "Pp3c2_17640V3.1" "Pp3c2_17670V3.1" "Pp3c2_17700V3.1"
[827] "Pp3c2_17710V3.1" "Pp3c2_17900V3.1" "Pp3c2_17910V3.1" "Pp3c2_18020V3.1" "Pp3c2_18030V3.1" "Pp3c2_18110V3.1" "Pp3c2_18130V3.1"
[834] "Pp3c2_18140V3.1" "Pp3c2_18330V3.1" "Pp3c2_18450V3.1" "Pp3c2_18480V3.1" "Pp3c2_18510V3.1" "Pp3c2_18520V3.1" "Pp3c2_18540V3.1"
[841] "Pp3c2_18570V3.1" "Pp3c2_18600V3.1" "Pp3c2_18610V3.1" "Pp3c2_18840V3.1" "Pp3c2_18850V3.1" "Pp3c2_18870V3.1" "Pp3c2_19150V3.1"
[848] "Pp3c2_19170V3.1" "Pp3c2_19250V3.1" "Pp3c2_19260V3.1" "Pp3c2_19310V3.1" "Pp3c2_19330V3.1" "Pp3c2_19380V3.1" "Pp3c2_19400V3.1"
[855] "Pp3c2_19430V3.1" "Pp3c2_19520V3.1" "Pp3c2_19550V3.1" "Pp3c2_19570V3.1" "Pp3c2_19610V3.1" "Pp3c2_19640V3.1" "Pp3c2_19660V3.1"
[862] "Pp3c2_19690V3.1" "Pp3c2_19700V3.1" "Pp3c2_19780V3.1" "Pp3c2_19940V3.1" "Pp3c2_19950V3.1" "Pp3c2_19980V3.1" "Pp3c2_20030V3.1"
[869] "Pp3c2_20120V3.1" "Pp3c2_20130V3.1" "Pp3c2_20141V3.1" "Pp3c2_20240V3.1" "Pp3c2_20320V3.1" "Pp3c2_20330V3.1" "Pp3c2_20450V3.1"
[876] "Pp3c2_20500V3.1" "Pp3c2_20550V3.1" "Pp3c2_20630V3.1" "Pp3c2_20660V3.1" "Pp3c2_20840V3.1" "Pp3c2_20860V3.1" "Pp3c2_20930V3.1"
[883] "Pp3c2_21100V3.1" "Pp3c2_21270V3.1" "Pp3c2_21290V3.1" "Pp3c2_21310V3.1" "Pp3c2_21370V3.1" "Pp3c2_21470V3.1" "Pp3c2_21580V3.1"
[890] "Pp3c2_21600V3.1" "Pp3c2_21660V3.1" "Pp3c2_21670V3.1" "Pp3c2_21710V3.1" "Pp3c2_21720V3.1" "Pp3c2_21940V3.1" "Pp3c2_21970V3.1"
[897] "Pp3c2_22000V3.1" "Pp3c2_22020V3.1" "Pp3c2_22140V3.1" "Pp3c2_22190V3.1" "Pp3c2_22570V3.1" "Pp3c2_22630V3.1" "Pp3c2_23100V3.1"
[904] "Pp3c2_23140V3.1" "Pp3c2_23200V3.1" "Pp3c2_23290V3.1" "Pp3c2_23300V3.1" "Pp3c2_23320V3.1" "Pp3c2_23750V3.1" "Pp3c2_23860V3.1"
[911] "Pp3c2_23870V3.1" "Pp3c2_23900V3.1" "Pp3c2_24110V3.1" "Pp3c2_24130V3.1" "Pp3c2_24150V3.1" "Pp3c2_24160V3.1" "Pp3c2_24230V3.1"
[918] "Pp3c2_24270V3.1" "Pp3c2_24500V3.1" "Pp3c2_24620V3.1" "Pp3c2_24640V3.1" "Pp3c2_24670V3.1" "Pp3c2_24723V3.1" "Pp3c2_24761V3.1"
[925] "Pp3c2_24840V3.1" "Pp3c2_24870V3.1" "Pp3c2_24910V3.1" "Pp3c2_25000V3.1" "Pp3c2_25170V3.1" "Pp3c2_25440V3.1" "Pp3c2_25580V3.1"
[932] "Pp3c2_25690V3.1" "Pp3c2_25760V3.1" "Pp3c2_25890V3.1" "Pp3c2_25930V3.1" "Pp3c2_26060V3.1" "Pp3c2_26200V3.1" "Pp3c2_26250V3.1"
[939] "Pp3c2_26270V3.1" "Pp3c2_26320V3.1" "Pp3c2_26540V3.1" "Pp3c2_26650V3.1" "Pp3c2_26700V3.1" "Pp3c2_26720V3.1" "Pp3c2_26890V3.1"
[946] "Pp3c2_27120V3.1" "Pp3c2_27180V3.1" "Pp3c2_27270V3.1" "Pp3c2_27310V3.1" "Pp3c2_27320V3.1" "Pp3c2_27330V3.1" "Pp3c2_27340V3.1"
[953] "Pp3c2_27350V3.1" "Pp3c2_27440V3.1" "Pp3c2_27510V3.1" "Pp3c2_27540V3.1" "Pp3c2_27550V3.1" "Pp3c2_27590V3.1" "Pp3c2_27820V3.1"
[960] "Pp3c2_27880V3.1" "Pp3c2_27910V3.1" "Pp3c2_27940V3.1" "Pp3c2_28030V3.1" "Pp3c2_28040V3.1" "Pp3c2_28070V3.1" "Pp3c2_28130V3.1"
[967] "Pp3c2_28140V3.1" "Pp3c2_28180V3.1" "Pp3c2_28280V3.1" "Pp3c2_28380V3.1" "Pp3c2_28420V3.1" "Pp3c2_28540V3.1" "Pp3c2_28550V3.1"
[974] "Pp3c2_28570V3.1" "Pp3c2_28690V3.1" "Pp3c2_28870V3.1" "Pp3c2_28950V3.1" "Pp3c2_29040V3.1" "Pp3c2_29090V3.1" "Pp3c2_29140V3.1"
[981] "Pp3c2_29249V3.1" "Pp3c2_29290V3.1" "Pp3c2_29420V3.1" "Pp3c2_29500V3.1" "Pp3c2_29560V3.1" "Pp3c2_29570V3.1" "Pp3c2_29720V3.1"
[988] "Pp3c2_29800V3.1" "Pp3c2_29840V3.1" "Pp3c2_29920V3.1" "Pp3c2_30010V3.1" "Pp3c2_30030V3.1" "Pp3c2_30230V3.1" "Pp3c2_30250V3.1"
[995] "Pp3c2_30340V3.1" "Pp3c2_30370V3.1" "Pp3c2_30390V3.1" "Pp3c2_30500V3.1" "Pp3c2_30510V3.1" "Pp3c2_30530V3.1"
[ reached getOption("max.print") -- omitted 7440 entries ]
[1] "DEGs intersection with direction check"
[1] 8440
[1] "Pp3c1_40V3.1" "Pp3c1_70V3.1" "Pp3c1_100V3.1" "Pp3c1_200V3.1" "Pp3c1_370V3.1" "Pp3c1_400V3.1" "Pp3c1_470V3.1"
[8] "Pp3c1_540V3.1" "Pp3c1_580V3.1" "Pp3c1_620V3.1" "Pp3c1_680V3.1" "Pp3c1_690V3.1" "Pp3c1_890V3.1" "Pp3c1_900V3.1"
[15] "Pp3c1_950V3.1" "Pp3c1_1000V3.1" "Pp3c1_1160V3.1" "Pp3c1_1240V3.1" "Pp3c1_1260V3.1" "Pp3c1_1330V3.1" "Pp3c1_1390V3.1"
[22] "Pp3c1_1570V3.1" "Pp3c1_1650V3.1" "Pp3c1_1790V3.1" "Pp3c1_1800V3.1" "Pp3c1_1810V3.1" "Pp3c1_1860V3.1" "Pp3c1_1870V3.1"
[29] "Pp3c1_1940V3.1" "Pp3c1_2010V3.1" "Pp3c1_2170V3.1" "Pp3c1_2210V3.1" "Pp3c1_2220V3.1" "Pp3c1_2420V3.1" "Pp3c1_2540V3.1"
[36] "Pp3c1_2740V3.1" "Pp3c1_2920V3.1" "Pp3c1_2980V3.1" "Pp3c1_3000V3.1" "Pp3c1_3040V3.1" "Pp3c1_3140V3.1" "Pp3c1_3160V3.1"
[43] "Pp3c1_3180V3.1" "Pp3c1_3200V3.1" "Pp3c1_3210V3.1" "Pp3c1_3220V3.1" "Pp3c1_3230V3.1" "Pp3c1_3260V3.1" "Pp3c1_3300V3.1"
[50] "Pp3c1_3440V3.1" "Pp3c1_3500V3.1" "Pp3c1_3590V3.1" "Pp3c1_3610V3.1" "Pp3c1_3700V3.1" "Pp3c1_3730V3.1" "Pp3c1_3750V3.1"
[57] "Pp3c1_3890V3.1" "Pp3c1_4010V3.1" "Pp3c1_4030V3.1" "Pp3c1_4050V3.1" "Pp3c1_4120V3.1" "Pp3c1_4140V3.1" "Pp3c1_4180V3.1"
[64] "Pp3c1_4270V3.1" "Pp3c1_4350V3.1" "Pp3c1_4400V3.1" "Pp3c1_4470V3.1" "Pp3c1_4510V3.1" "Pp3c1_4540V3.1" "Pp3c1_4600V3.1"
[71] "Pp3c1_4750V3.1" "Pp3c1_4990V3.1" "Pp3c1_5050V3.1" "Pp3c1_5280V3.1" "Pp3c1_5300V3.1" "Pp3c1_5320V3.1" "Pp3c1_5460V3.1"
[78] "Pp3c1_5570V3.1" "Pp3c1_5800V3.1" "Pp3c1_5820V3.1" "Pp3c1_5850V3.1" "Pp3c1_5870V3.1" "Pp3c1_6020V3.1" "Pp3c1_6050V3.1"
[85] "Pp3c1_6090V3.1" "Pp3c1_6110V3.1" "Pp3c1_6130V3.1" "Pp3c1_6280V3.1" "Pp3c1_6360V3.1" "Pp3c1_6380V3.1" "Pp3c1_6450V3.1"
[92] "Pp3c1_6470V3.1" "Pp3c1_6480V3.1" "Pp3c1_6500V3.1" "Pp3c1_6570V3.1" "Pp3c1_6750V3.1" "Pp3c1_6930V3.1" "Pp3c1_6950V3.1"
[99] "Pp3c1_7010V3.1" "Pp3c1_7030V3.1" "Pp3c1_7090V3.1" "Pp3c1_7160V3.1" "Pp3c1_7220V3.1" "Pp3c1_7300V3.1" "Pp3c1_7360V3.1"
[106] "Pp3c1_7370V3.1" "Pp3c1_7380V3.1" "Pp3c1_7390V3.1" "Pp3c1_7450V3.1" "Pp3c1_7500V3.1" "Pp3c1_7520V3.1" "Pp3c1_7540V3.1"
[113] "Pp3c1_7590V3.1" "Pp3c1_7710V3.1" "Pp3c1_7720V3.1" "Pp3c1_7800V3.1" "Pp3c1_7810V3.1" "Pp3c1_7830V3.1" "Pp3c1_7880V3.1"
[120] "Pp3c1_7950V3.1" "Pp3c1_8060V3.1" "Pp3c1_8080V3.1" "Pp3c1_8110V3.1" "Pp3c1_8170V3.1" "Pp3c1_8190V3.1" "Pp3c1_8210V3.1"
[127] "Pp3c1_8240V3.1" "Pp3c1_8280V3.1" "Pp3c1_8450V3.1" "Pp3c1_8490V3.1" "Pp3c1_8530V3.1" "Pp3c1_8870V3.1" "Pp3c1_8890V3.1"
[134] "Pp3c1_9180V3.1" "Pp3c1_9250V3.1" "Pp3c1_9290V3.1" "Pp3c1_9320V3.1" "Pp3c1_9560V3.1" "Pp3c1_9600V3.1" "Pp3c1_9790V3.1"
[141] "Pp3c1_9970V3.1" "Pp3c1_10000V3.1" "Pp3c1_10010V3.1" "Pp3c1_10040V3.1" "Pp3c1_10080V3.1" "Pp3c1_10090V3.1" "Pp3c1_10100V3.1"
[148] "Pp3c1_10220V3.1" "Pp3c1_10400V3.1" "Pp3c1_10470V3.1" "Pp3c1_10530V3.1" "Pp3c1_10540V3.1" "Pp3c1_10570V3.1" "Pp3c1_10620V3.1"
[155] "Pp3c1_10630V3.1" "Pp3c1_10810V3.1" "Pp3c1_10880V3.1" "Pp3c1_10970V3.1" "Pp3c1_11030V3.1" "Pp3c1_11050V3.1" "Pp3c1_11090V3.1"
[162] "Pp3c1_11190V3.1" "Pp3c1_11980V3.1" "Pp3c1_12020V3.1" "Pp3c1_12100V3.1" "Pp3c1_12120V3.1" "Pp3c1_12140V3.1" "Pp3c1_12470V3.1"
[169] "Pp3c1_12560V3.1" "Pp3c1_12610V3.1" "Pp3c1_12630V3.1" "Pp3c1_12730V3.1" "Pp3c1_12790V3.1" "Pp3c1_12810V3.1" "Pp3c1_12850V3.1"
[176] "Pp3c1_12860V3.1" "Pp3c1_12940V3.1" "Pp3c1_13120V3.1" "Pp3c1_13170V3.1" "Pp3c1_13270V3.1" "Pp3c1_13308V3.1" "Pp3c1_13430V3.1"
[183] "Pp3c1_13570V3.1" "Pp3c1_13640V3.1" "Pp3c1_13670V3.1" "Pp3c1_13671V3.1" "Pp3c1_13800V3.1" "Pp3c1_13830V3.1" "Pp3c1_13890V3.1"
[190] "Pp3c1_13910V3.1" "Pp3c1_13930V3.1" "Pp3c1_14230V3.1" "Pp3c1_14330V3.1" "Pp3c1_14380V3.1" "Pp3c1_14540V3.1" "Pp3c1_14740V3.1"
[197] "Pp3c1_14760V3.1" "Pp3c1_14770V3.1" "Pp3c1_14800V3.1" "Pp3c1_14870V3.1" "Pp3c1_14910V3.1" "Pp3c1_14920V3.1" "Pp3c1_14980V3.1"
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[729] "Pp3c2_11250V3.1" "Pp3c2_11370V3.1" "Pp3c2_11380V3.1" "Pp3c2_11410V3.1" "Pp3c2_11490V3.1" "Pp3c2_11580V3.1" "Pp3c2_11670V3.1"
[736] "Pp3c2_11730V3.1" "Pp3c2_11820V3.1" "Pp3c2_11870V3.1" "Pp3c2_11890V3.1" "Pp3c2_12080V3.1" "Pp3c2_12120V3.1" "Pp3c2_12150V3.1"
[743] "Pp3c2_12240V3.1" "Pp3c2_12290V3.1" "Pp3c2_12370V3.1" "Pp3c2_12550V3.1" "Pp3c2_12620V3.1" "Pp3c2_12640V3.1" "Pp3c2_12670V3.1"
[750] "Pp3c2_12680V3.1" "Pp3c2_13250V3.1" "Pp3c2_13270V3.1" "Pp3c2_13280V3.1" "Pp3c2_13290V3.1" "Pp3c2_13330V3.1" "Pp3c2_13400V3.1"
[757] "Pp3c2_13410V3.1" "Pp3c2_13420V3.1" "Pp3c2_13450V3.1" "Pp3c2_13560V3.1" "Pp3c2_13590V3.1" "Pp3c2_13670V3.1" "Pp3c2_13790V3.1"
[764] "Pp3c2_13820V3.1" "Pp3c2_13870V3.1" "Pp3c2_13880V3.1" "Pp3c2_13930V3.1" "Pp3c2_13970V3.1" "Pp3c2_14060V3.1" "Pp3c2_14090V3.1"
[771] "Pp3c2_14120V3.1" "Pp3c2_14270V3.1" "Pp3c2_14290V3.1" "Pp3c2_14350V3.1" "Pp3c2_14400V3.1" "Pp3c2_14410V3.1" "Pp3c2_14470V3.1"
[778] "Pp3c2_14520V3.1" "Pp3c2_14560V3.1" "Pp3c2_14570V3.1" "Pp3c2_14600V3.1" "Pp3c2_14610V3.1" "Pp3c2_14800V3.1" "Pp3c2_14820V3.1"
[785] "Pp3c2_14930V3.1" "Pp3c2_15060V3.1" "Pp3c2_15140V3.1" "Pp3c2_15180V3.1" "Pp3c2_15200V3.1" "Pp3c2_15250V3.1" "Pp3c2_15400V3.1"
[792] "Pp3c2_15430V3.1" "Pp3c2_15480V3.1" "Pp3c2_15490V3.1" "Pp3c2_15500V3.1" "Pp3c2_15510V3.1" "Pp3c2_15820V3.1" "Pp3c2_15900V3.1"
[799] "Pp3c2_15910V3.1" "Pp3c2_15950V3.1" "Pp3c2_16030V3.1" "Pp3c2_16160V3.1" "Pp3c2_16250V3.1" "Pp3c2_16300V3.1" "Pp3c2_16310V3.1"
[806] "Pp3c2_16610V3.1" "Pp3c2_16660V3.1" "Pp3c2_16770V3.1" "Pp3c2_16800V3.1" "Pp3c2_16830V3.1" "Pp3c2_17000V3.1" "Pp3c2_17040V3.1"
[813] "Pp3c2_17110V3.1" "Pp3c2_17140V3.1" "Pp3c2_17270V3.1" "Pp3c2_17290V3.1" "Pp3c2_17370V3.1" "Pp3c2_17380V3.1" "Pp3c2_17390V3.1"
[820] "Pp3c2_17450V3.1" "Pp3c2_17510V3.1" "Pp3c2_17540V3.1" "Pp3c2_17560V3.1" "Pp3c2_17640V3.1" "Pp3c2_17670V3.1" "Pp3c2_17700V3.1"
[827] "Pp3c2_17710V3.1" "Pp3c2_17900V3.1" "Pp3c2_17910V3.1" "Pp3c2_18020V3.1" "Pp3c2_18030V3.1" "Pp3c2_18110V3.1" "Pp3c2_18130V3.1"
[834] "Pp3c2_18140V3.1" "Pp3c2_18330V3.1" "Pp3c2_18450V3.1" "Pp3c2_18480V3.1" "Pp3c2_18510V3.1" "Pp3c2_18520V3.1" "Pp3c2_18540V3.1"
[841] "Pp3c2_18570V3.1" "Pp3c2_18600V3.1" "Pp3c2_18610V3.1" "Pp3c2_18840V3.1" "Pp3c2_18850V3.1" "Pp3c2_18870V3.1" "Pp3c2_19150V3.1"
[848] "Pp3c2_19170V3.1" "Pp3c2_19250V3.1" "Pp3c2_19260V3.1" "Pp3c2_19310V3.1" "Pp3c2_19330V3.1" "Pp3c2_19380V3.1" "Pp3c2_19400V3.1"
[855] "Pp3c2_19430V3.1" "Pp3c2_19520V3.1" "Pp3c2_19550V3.1" "Pp3c2_19570V3.1" "Pp3c2_19610V3.1" "Pp3c2_19640V3.1" "Pp3c2_19660V3.1"
[862] "Pp3c2_19690V3.1" "Pp3c2_19700V3.1" "Pp3c2_19780V3.1" "Pp3c2_19940V3.1" "Pp3c2_19950V3.1" "Pp3c2_19980V3.1" "Pp3c2_20030V3.1"
[869] "Pp3c2_20120V3.1" "Pp3c2_20130V3.1" "Pp3c2_20141V3.1" "Pp3c2_20240V3.1" "Pp3c2_20320V3.1" "Pp3c2_20330V3.1" "Pp3c2_20450V3.1"
[876] "Pp3c2_20500V3.1" "Pp3c2_20550V3.1" "Pp3c2_20630V3.1" "Pp3c2_20660V3.1" "Pp3c2_20840V3.1" "Pp3c2_20860V3.1" "Pp3c2_20930V3.1"
[883] "Pp3c2_21100V3.1" "Pp3c2_21270V3.1" "Pp3c2_21290V3.1" "Pp3c2_21310V3.1" "Pp3c2_21370V3.1" "Pp3c2_21470V3.1" "Pp3c2_21580V3.1"
[890] "Pp3c2_21600V3.1" "Pp3c2_21660V3.1" "Pp3c2_21670V3.1" "Pp3c2_21710V3.1" "Pp3c2_21720V3.1" "Pp3c2_21940V3.1" "Pp3c2_21970V3.1"
[897] "Pp3c2_22000V3.1" "Pp3c2_22020V3.1" "Pp3c2_22140V3.1" "Pp3c2_22190V3.1" "Pp3c2_22570V3.1" "Pp3c2_22630V3.1" "Pp3c2_23100V3.1"
[904] "Pp3c2_23140V3.1" "Pp3c2_23200V3.1" "Pp3c2_23290V3.1" "Pp3c2_23300V3.1" "Pp3c2_23320V3.1" "Pp3c2_23750V3.1" "Pp3c2_23860V3.1"
[911] "Pp3c2_23870V3.1" "Pp3c2_23900V3.1" "Pp3c2_24110V3.1" "Pp3c2_24130V3.1" "Pp3c2_24150V3.1" "Pp3c2_24160V3.1" "Pp3c2_24230V3.1"
[918] "Pp3c2_24270V3.1" "Pp3c2_24500V3.1" "Pp3c2_24620V3.1" "Pp3c2_24640V3.1" "Pp3c2_24670V3.1" "Pp3c2_24723V3.1" "Pp3c2_24761V3.1"
[925] "Pp3c2_24840V3.1" "Pp3c2_24870V3.1" "Pp3c2_24910V3.1" "Pp3c2_25000V3.1" "Pp3c2_25170V3.1" "Pp3c2_25440V3.1" "Pp3c2_25580V3.1"
[932] "Pp3c2_25690V3.1" "Pp3c2_25760V3.1" "Pp3c2_25890V3.1" "Pp3c2_25930V3.1" "Pp3c2_26060V3.1" "Pp3c2_26200V3.1" "Pp3c2_26250V3.1"
[939] "Pp3c2_26270V3.1" "Pp3c2_26320V3.1" "Pp3c2_26540V3.1" "Pp3c2_26650V3.1" "Pp3c2_26700V3.1" "Pp3c2_26720V3.1" "Pp3c2_26890V3.1"
[946] "Pp3c2_27120V3.1" "Pp3c2_27180V3.1" "Pp3c2_27270V3.1" "Pp3c2_27310V3.1" "Pp3c2_27320V3.1" "Pp3c2_27330V3.1" "Pp3c2_27340V3.1"
[953] "Pp3c2_27350V3.1" "Pp3c2_27440V3.1" "Pp3c2_27510V3.1" "Pp3c2_27540V3.1" "Pp3c2_27550V3.1" "Pp3c2_27590V3.1" "Pp3c2_27820V3.1"
[960] "Pp3c2_27880V3.1" "Pp3c2_27910V3.1" "Pp3c2_27940V3.1" "Pp3c2_28030V3.1" "Pp3c2_28040V3.1" "Pp3c2_28070V3.1" "Pp3c2_28130V3.1"
[967] "Pp3c2_28140V3.1" "Pp3c2_28180V3.1" "Pp3c2_28280V3.1" "Pp3c2_28380V3.1" "Pp3c2_28420V3.1" "Pp3c2_28540V3.1" "Pp3c2_28550V3.1"
[974] "Pp3c2_28570V3.1" "Pp3c2_28690V3.1" "Pp3c2_28870V3.1" "Pp3c2_28950V3.1" "Pp3c2_29040V3.1" "Pp3c2_29090V3.1" "Pp3c2_29140V3.1"
[981] "Pp3c2_29249V3.1" "Pp3c2_29290V3.1" "Pp3c2_29420V3.1" "Pp3c2_29500V3.1" "Pp3c2_29560V3.1" "Pp3c2_29570V3.1" "Pp3c2_29720V3.1"
[988] "Pp3c2_29800V3.1" "Pp3c2_29840V3.1" "Pp3c2_29920V3.1" "Pp3c2_30010V3.1" "Pp3c2_30030V3.1" "Pp3c2_30230V3.1" "Pp3c2_30250V3.1"
[995] "Pp3c2_30340V3.1" "Pp3c2_30370V3.1" "Pp3c2_30390V3.1" "Pp3c2_30500V3.1" "Pp3c2_30510V3.1" "Pp3c2_30530V3.1"
[ reached getOption("max.print") -- omitted 7440 entries ]
[1] "DEGs edgeR"
[1] 14109
[1] "DEGs deseq2"
[1] 12443
[1] "DEGs noiseq"
[1] 8635
[1] "DEGs noiseqbio"
[1] 10391
[1] "DEGs intersection without direction check (three methods)"
[1] 8578
[1] "Pp3c1_40V3.1" "Pp3c1_70V3.1" "Pp3c1_100V3.1" "Pp3c1_200V3.1" "Pp3c1_370V3.1" "Pp3c1_400V3.1" "Pp3c1_470V3.1"
[8] "Pp3c1_540V3.1" "Pp3c1_580V3.1" "Pp3c1_620V3.1" "Pp3c1_680V3.1" "Pp3c1_690V3.1" "Pp3c1_890V3.1" "Pp3c1_900V3.1"
[15] "Pp3c1_950V3.1" "Pp3c1_1000V3.1" "Pp3c1_1160V3.1" "Pp3c1_1240V3.1" "Pp3c1_1260V3.1" "Pp3c1_1330V3.1" "Pp3c1_1390V3.1"
[22] "Pp3c1_1570V3.1" "Pp3c1_1650V3.1" "Pp3c1_1790V3.1" "Pp3c1_1800V3.1" "Pp3c1_1810V3.1" "Pp3c1_1860V3.1" "Pp3c1_1870V3.1"
[29] "Pp3c1_1940V3.1" "Pp3c1_2010V3.1" "Pp3c1_2170V3.1" "Pp3c1_2210V3.1" "Pp3c1_2220V3.1" "Pp3c1_2420V3.1" "Pp3c1_2540V3.1"
[36] "Pp3c1_2740V3.1" "Pp3c1_2920V3.1" "Pp3c1_2980V3.1" "Pp3c1_3000V3.1" "Pp3c1_3040V3.1" "Pp3c1_3140V3.1" "Pp3c1_3160V3.1"
[43] "Pp3c1_3180V3.1" "Pp3c1_3200V3.1" "Pp3c1_3210V3.1" "Pp3c1_3220V3.1" "Pp3c1_3230V3.1" "Pp3c1_3260V3.1" "Pp3c1_3300V3.1"
[50] "Pp3c1_3440V3.1" "Pp3c1_3500V3.1" "Pp3c1_3590V3.1" "Pp3c1_3610V3.1" "Pp3c1_3700V3.1" "Pp3c1_3730V3.1" "Pp3c1_3750V3.1"
[57] "Pp3c1_3890V3.1" "Pp3c1_4010V3.1" "Pp3c1_4030V3.1" "Pp3c1_4050V3.1" "Pp3c1_4120V3.1" "Pp3c1_4140V3.1" "Pp3c1_4180V3.1"
[64] "Pp3c1_4270V3.1" "Pp3c1_4350V3.1" "Pp3c1_4400V3.1" "Pp3c1_4470V3.1" "Pp3c1_4510V3.1" "Pp3c1_4540V3.1" "Pp3c1_4600V3.1"
[71] "Pp3c1_4750V3.1" "Pp3c1_4990V3.1" "Pp3c1_5050V3.1" "Pp3c1_5280V3.1" "Pp3c1_5300V3.1" "Pp3c1_5320V3.1" "Pp3c1_5460V3.1"
[78] "Pp3c1_5570V3.1" "Pp3c1_5800V3.1" "Pp3c1_5820V3.1" "Pp3c1_5850V3.1" "Pp3c1_5870V3.1" "Pp3c1_6020V3.1" "Pp3c1_6050V3.1"
[85] "Pp3c1_6090V3.1" "Pp3c1_6110V3.1" "Pp3c1_6130V3.1" "Pp3c1_6280V3.1" "Pp3c1_6360V3.1" "Pp3c1_6380V3.1" "Pp3c1_6450V3.1"
[92] "Pp3c1_6470V3.1" "Pp3c1_6480V3.1" "Pp3c1_6500V3.1" "Pp3c1_6570V3.1" "Pp3c1_6750V3.1" "Pp3c1_6930V3.1" "Pp3c1_6950V3.1"
[99] "Pp3c1_7010V3.1" "Pp3c1_7030V3.1" "Pp3c1_7090V3.1" "Pp3c1_7160V3.1" "Pp3c1_7220V3.1" "Pp3c1_7300V3.1" "Pp3c1_7360V3.1"
[106] "Pp3c1_7370V3.1" "Pp3c1_7380V3.1" "Pp3c1_7390V3.1" "Pp3c1_7450V3.1" "Pp3c1_7500V3.1" "Pp3c1_7520V3.1" "Pp3c1_7540V3.1"
[113] "Pp3c1_7590V3.1" "Pp3c1_7710V3.1" "Pp3c1_7720V3.1" "Pp3c1_7800V3.1" "Pp3c1_7810V3.1" "Pp3c1_7830V3.1" "Pp3c1_7880V3.1"
[120] "Pp3c1_7950V3.1" "Pp3c1_8060V3.1" "Pp3c1_8080V3.1" "Pp3c1_8110V3.1" "Pp3c1_8170V3.1" "Pp3c1_8190V3.1" "Pp3c1_8210V3.1"
[127] "Pp3c1_8240V3.1" "Pp3c1_8280V3.1" "Pp3c1_8450V3.1" "Pp3c1_8490V3.1" "Pp3c1_8530V3.1" "Pp3c1_8870V3.1" "Pp3c1_8890V3.1"
[134] "Pp3c1_9180V3.1" "Pp3c1_9190V3.1" "Pp3c1_9250V3.1" "Pp3c1_9290V3.1" "Pp3c1_9320V3.1" "Pp3c1_9560V3.1" "Pp3c1_9600V3.1"
[141] "Pp3c1_9790V3.1" "Pp3c1_9860V3.1" "Pp3c1_9970V3.1" "Pp3c1_10000V3.1" "Pp3c1_10010V3.1" "Pp3c1_10040V3.1" "Pp3c1_10080V3.1"
[148] "Pp3c1_10090V3.1" "Pp3c1_10100V3.1" "Pp3c1_10220V3.1" "Pp3c1_10400V3.1" "Pp3c1_10470V3.1" "Pp3c1_10530V3.1" "Pp3c1_10540V3.1"
[155] "Pp3c1_10570V3.1" "Pp3c1_10620V3.1" "Pp3c1_10630V3.1" "Pp3c1_10810V3.1" "Pp3c1_10880V3.1" "Pp3c1_10970V3.1" "Pp3c1_11030V3.1"
[162] "Pp3c1_11050V3.1" "Pp3c1_11090V3.1" "Pp3c1_11190V3.1" "Pp3c1_11980V3.1" "Pp3c1_12020V3.1" "Pp3c1_12100V3.1" "Pp3c1_12120V3.1"
[169] "Pp3c1_12140V3.1" "Pp3c1_12470V3.1" "Pp3c1_12560V3.1" "Pp3c1_12610V3.1" "Pp3c1_12630V3.1" "Pp3c1_12730V3.1" "Pp3c1_12790V3.1"
[176] "Pp3c1_12810V3.1" "Pp3c1_12850V3.1" "Pp3c1_12860V3.1" "Pp3c1_12940V3.1" "Pp3c1_13120V3.1" "Pp3c1_13170V3.1" "Pp3c1_13270V3.1"
[183] "Pp3c1_13308V3.1" "Pp3c1_13430V3.1" "Pp3c1_13570V3.1" "Pp3c1_13640V3.1" "Pp3c1_13670V3.1" "Pp3c1_13671V3.1" "Pp3c1_13800V3.1"
[190] "Pp3c1_13830V3.1" "Pp3c1_13890V3.1" "Pp3c1_13910V3.1" "Pp3c1_13930V3.1" "Pp3c1_14230V3.1" "Pp3c1_14330V3.1" "Pp3c1_14380V3.1"
[197] "Pp3c1_14540V3.1" "Pp3c1_14740V3.1" "Pp3c1_14760V3.1" "Pp3c1_14770V3.1" "Pp3c1_14800V3.1" "Pp3c1_14870V3.1" "Pp3c1_14910V3.1"
[204] "Pp3c1_14920V3.1" "Pp3c1_14980V3.1" "Pp3c1_15010V3.1" "Pp3c1_15090V3.1" "Pp3c1_15100V3.1" "Pp3c1_15110V3.1" "Pp3c1_15150V3.1"
[211] "Pp3c1_15160V3.1" "Pp3c1_15210V3.1" "Pp3c1_15400V3.1" "Pp3c1_15410V3.1" "Pp3c1_15460V3.1" "Pp3c1_15560V3.1" "Pp3c1_15690V3.1"
[218] "Pp3c1_15730V3.1" "Pp3c1_15750V3.1" "Pp3c1_15940V3.1" "Pp3c1_16170V3.1" "Pp3c1_16250V3.1" "Pp3c1_16500V3.1" "Pp3c1_16600V3.1"
[225] "Pp3c1_16780V3.1" "Pp3c1_16840V3.1" "Pp3c1_16850V3.1" "Pp3c1_16900V3.1" "Pp3c1_16980V3.1" "Pp3c1_17080V3.1" "Pp3c1_17220V3.1"
[232] "Pp3c1_17710V3.1" "Pp3c1_17860V3.1" "Pp3c1_18050V3.1" "Pp3c1_18130V3.1" "Pp3c1_18150V3.1" "Pp3c1_18250V3.1" "Pp3c1_18260V3.1"
[239] "Pp3c1_18440V3.1" "Pp3c1_18460V3.1" "Pp3c1_18530V3.1" "Pp3c1_18680V3.1" "Pp3c1_18830V3.1" "Pp3c1_18860V3.1" "Pp3c1_18910V3.1"
[246] "Pp3c1_18940V3.1" "Pp3c1_19060V3.1" "Pp3c1_19190V3.1" "Pp3c1_19200V3.1" "Pp3c1_19210V3.1" "Pp3c1_19230V3.1" "Pp3c1_19240V3.1"
[253] "Pp3c1_19310V3.1" "Pp3c1_19370V3.1" "Pp3c1_19400V3.1" "Pp3c1_19660V3.1" "Pp3c1_19950V3.1" "Pp3c1_20100V3.1" "Pp3c1_20280V3.1"
[260] "Pp3c1_20310V3.1" "Pp3c1_20350V3.1" "Pp3c1_20430V3.1" "Pp3c1_20630V3.1" "Pp3c1_20640V3.1" "Pp3c1_20690V3.1" "Pp3c1_20700V3.1"
[267] "Pp3c1_20710V3.1" "Pp3c1_20753V3.1" "Pp3c1_20770V3.1" "Pp3c1_20790V3.1" "Pp3c1_20810V3.1" "Pp3c1_20870V3.1" "Pp3c1_20880V3.1"
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[799] "Pp3c2_15430V3.1" "Pp3c2_15480V3.1" "Pp3c2_15490V3.1" "Pp3c2_15500V3.1" "Pp3c2_15510V3.1" "Pp3c2_15820V3.1" "Pp3c2_15900V3.1"
[806] "Pp3c2_15910V3.1" "Pp3c2_15950V3.1" "Pp3c2_16030V3.1" "Pp3c2_16160V3.1" "Pp3c2_16250V3.1" "Pp3c2_16300V3.1" "Pp3c2_16310V3.1"
[813] "Pp3c2_16610V3.1" "Pp3c2_16660V3.1" "Pp3c2_16770V3.1" "Pp3c2_16800V3.1" "Pp3c2_16830V3.1" "Pp3c2_17000V3.1" "Pp3c2_17040V3.1"
[820] "Pp3c2_17110V3.1" "Pp3c2_17140V3.1" "Pp3c2_17270V3.1" "Pp3c2_17290V3.1" "Pp3c2_17370V3.1" "Pp3c2_17380V3.1" "Pp3c2_17390V3.1"
[827] "Pp3c2_17450V3.1" "Pp3c2_17510V3.1" "Pp3c2_17540V3.1" "Pp3c2_17560V3.1" "Pp3c2_17640V3.1" "Pp3c2_17670V3.1" "Pp3c2_17700V3.1"
[834] "Pp3c2_17710V3.1" "Pp3c2_17900V3.1" "Pp3c2_17910V3.1" "Pp3c2_18020V3.1" "Pp3c2_18030V3.1" "Pp3c2_18110V3.1" "Pp3c2_18130V3.1"
[841] "Pp3c2_18140V3.1" "Pp3c2_18330V3.1" "Pp3c2_18450V3.1" "Pp3c2_18480V3.1" "Pp3c2_18510V3.1" "Pp3c2_18520V3.1" "Pp3c2_18540V3.1"
[848] "Pp3c2_18570V3.1" "Pp3c2_18600V3.1" "Pp3c2_18610V3.1" "Pp3c2_18840V3.1" "Pp3c2_18850V3.1" "Pp3c2_18870V3.1" "Pp3c2_19150V3.1"
[855] "Pp3c2_19170V3.1" "Pp3c2_19250V3.1" "Pp3c2_19260V3.1" "Pp3c2_19310V3.1" "Pp3c2_19330V3.1" "Pp3c2_19380V3.1" "Pp3c2_19400V3.1"
[862] "Pp3c2_19430V3.1" "Pp3c2_19520V3.1" "Pp3c2_19550V3.1" "Pp3c2_19570V3.1" "Pp3c2_19610V3.1" "Pp3c2_19640V3.1" "Pp3c2_19660V3.1"
[869] "Pp3c2_19690V3.1" "Pp3c2_19700V3.1" "Pp3c2_19780V3.1" "Pp3c2_19940V3.1" "Pp3c2_19950V3.1" "Pp3c2_19980V3.1" "Pp3c2_20030V3.1"
[876] "Pp3c2_20120V3.1" "Pp3c2_20130V3.1" "Pp3c2_20141V3.1" "Pp3c2_20240V3.1" "Pp3c2_20320V3.1" "Pp3c2_20330V3.1" "Pp3c2_20450V3.1"
[883] "Pp3c2_20500V3.1" "Pp3c2_20550V3.1" "Pp3c2_20630V3.1" "Pp3c2_20660V3.1" "Pp3c2_20840V3.1" "Pp3c2_20860V3.1" "Pp3c2_20930V3.1"
[890] "Pp3c2_21100V3.1" "Pp3c2_21270V3.1" "Pp3c2_21290V3.1" "Pp3c2_21310V3.1" "Pp3c2_21370V3.1" "Pp3c2_21470V3.1" "Pp3c2_21580V3.1"
[897] "Pp3c2_21600V3.1" "Pp3c2_21660V3.1" "Pp3c2_21670V3.1" "Pp3c2_21710V3.1" "Pp3c2_21720V3.1" "Pp3c2_21940V3.1" "Pp3c2_21970V3.1"
[904] "Pp3c2_22000V3.1" "Pp3c2_22020V3.1" "Pp3c2_22140V3.1" "Pp3c2_22190V3.1" "Pp3c2_22570V3.1" "Pp3c2_22630V3.1" "Pp3c2_23100V3.1"
[911] "Pp3c2_23140V3.1" "Pp3c2_23200V3.1" "Pp3c2_23290V3.1" "Pp3c2_23300V3.1" "Pp3c2_23320V3.1" "Pp3c2_23750V3.1" "Pp3c2_23860V3.1"
[918] "Pp3c2_23870V3.1" "Pp3c2_23900V3.1" "Pp3c2_24110V3.1" "Pp3c2_24130V3.1" "Pp3c2_24150V3.1" "Pp3c2_24160V3.1" "Pp3c2_24230V3.1"
[925] "Pp3c2_24270V3.1" "Pp3c2_24500V3.1" "Pp3c2_24620V3.1" "Pp3c2_24640V3.1" "Pp3c2_24670V3.1" "Pp3c2_24723V3.1" "Pp3c2_24761V3.1"
[932] "Pp3c2_24840V3.1" "Pp3c2_24870V3.1" "Pp3c2_24910V3.1" "Pp3c2_25000V3.1" "Pp3c2_25170V3.1" "Pp3c2_25440V3.1" "Pp3c2_25580V3.1"
[939] "Pp3c2_25690V3.1" "Pp3c2_25760V3.1" "Pp3c2_25890V3.1" "Pp3c2_25930V3.1" "Pp3c2_26060V3.1" "Pp3c2_26200V3.1" "Pp3c2_26250V3.1"
[946] "Pp3c2_26270V3.1" "Pp3c2_26320V3.1" "Pp3c2_26540V3.1" "Pp3c2_26650V3.1" "Pp3c2_26700V3.1" "Pp3c2_26720V3.1" "Pp3c2_26890V3.1"
[953] "Pp3c2_27120V3.1" "Pp3c2_27180V3.1" "Pp3c2_27270V3.1" "Pp3c2_27310V3.1" "Pp3c2_27320V3.1" "Pp3c2_27330V3.1" "Pp3c2_27340V3.1"
[960] "Pp3c2_27350V3.1" "Pp3c2_27440V3.1" "Pp3c2_27510V3.1" "Pp3c2_27540V3.1" "Pp3c2_27550V3.1" "Pp3c2_27590V3.1" "Pp3c2_27820V3.1"
[967] "Pp3c2_27880V3.1" "Pp3c2_27910V3.1" "Pp3c2_27940V3.1" "Pp3c2_27980V3.1" "Pp3c2_28010V3.1" "Pp3c2_28030V3.1" "Pp3c2_28040V3.1"
[974] "Pp3c2_28070V3.1" "Pp3c2_28130V3.1" "Pp3c2_28140V3.1" "Pp3c2_28180V3.1" "Pp3c2_28280V3.1" "Pp3c2_28380V3.1" "Pp3c2_28420V3.1"
[981] "Pp3c2_28540V3.1" "Pp3c2_28550V3.1" "Pp3c2_28570V3.1" "Pp3c2_28690V3.1" "Pp3c2_28870V3.1" "Pp3c2_28950V3.1" "Pp3c2_29040V3.1"
[988] "Pp3c2_29090V3.1" "Pp3c2_29140V3.1" "Pp3c2_29249V3.1" "Pp3c2_29290V3.1" "Pp3c2_29420V3.1" "Pp3c2_29500V3.1" "Pp3c2_29560V3.1"
[995] "Pp3c2_29570V3.1" "Pp3c2_29720V3.1" "Pp3c2_29800V3.1" "Pp3c2_29840V3.1" "Pp3c2_29920V3.1" "Pp3c2_30010V3.1"
[ reached getOption("max.print") -- omitted 7578 entries ]
[1] "DEGs intersection with direction check"
[1] 8578
[1] "Pp3c1_40V3.1" "Pp3c1_70V3.1" "Pp3c1_100V3.1" "Pp3c1_200V3.1" "Pp3c1_370V3.1" "Pp3c1_400V3.1" "Pp3c1_470V3.1"
[8] "Pp3c1_540V3.1" "Pp3c1_580V3.1" "Pp3c1_620V3.1" "Pp3c1_680V3.1" "Pp3c1_690V3.1" "Pp3c1_890V3.1" "Pp3c1_900V3.1"
[15] "Pp3c1_950V3.1" "Pp3c1_1000V3.1" "Pp3c1_1160V3.1" "Pp3c1_1240V3.1" "Pp3c1_1260V3.1" "Pp3c1_1330V3.1" "Pp3c1_1390V3.1"
[22] "Pp3c1_1570V3.1" "Pp3c1_1650V3.1" "Pp3c1_1790V3.1" "Pp3c1_1800V3.1" "Pp3c1_1810V3.1" "Pp3c1_1860V3.1" "Pp3c1_1870V3.1"
[29] "Pp3c1_1940V3.1" "Pp3c1_2010V3.1" "Pp3c1_2170V3.1" "Pp3c1_2210V3.1" "Pp3c1_2220V3.1" "Pp3c1_2420V3.1" "Pp3c1_2540V3.1"
[36] "Pp3c1_2740V3.1" "Pp3c1_2920V3.1" "Pp3c1_2980V3.1" "Pp3c1_3000V3.1" "Pp3c1_3040V3.1" "Pp3c1_3140V3.1" "Pp3c1_3160V3.1"
[43] "Pp3c1_3180V3.1" "Pp3c1_3200V3.1" "Pp3c1_3210V3.1" "Pp3c1_3220V3.1" "Pp3c1_3230V3.1" "Pp3c1_3260V3.1" "Pp3c1_3300V3.1"
[50] "Pp3c1_3440V3.1" "Pp3c1_3500V3.1" "Pp3c1_3590V3.1" "Pp3c1_3610V3.1" "Pp3c1_3700V3.1" "Pp3c1_3730V3.1" "Pp3c1_3750V3.1"
[57] "Pp3c1_3890V3.1" "Pp3c1_4010V3.1" "Pp3c1_4030V3.1" "Pp3c1_4050V3.1" "Pp3c1_4120V3.1" "Pp3c1_4140V3.1" "Pp3c1_4180V3.1"
[64] "Pp3c1_4270V3.1" "Pp3c1_4350V3.1" "Pp3c1_4400V3.1" "Pp3c1_4470V3.1" "Pp3c1_4510V3.1" "Pp3c1_4540V3.1" "Pp3c1_4600V3.1"
[71] "Pp3c1_4750V3.1" "Pp3c1_4990V3.1" "Pp3c1_5050V3.1" "Pp3c1_5280V3.1" "Pp3c1_5300V3.1" "Pp3c1_5320V3.1" "Pp3c1_5460V3.1"
[78] "Pp3c1_5570V3.1" "Pp3c1_5800V3.1" "Pp3c1_5820V3.1" "Pp3c1_5850V3.1" "Pp3c1_5870V3.1" "Pp3c1_6020V3.1" "Pp3c1_6050V3.1"
[85] "Pp3c1_6090V3.1" "Pp3c1_6110V3.1" "Pp3c1_6130V3.1" "Pp3c1_6280V3.1" "Pp3c1_6360V3.1" "Pp3c1_6380V3.1" "Pp3c1_6450V3.1"
[92] "Pp3c1_6470V3.1" "Pp3c1_6480V3.1" "Pp3c1_6500V3.1" "Pp3c1_6570V3.1" "Pp3c1_6750V3.1" "Pp3c1_6930V3.1" "Pp3c1_6950V3.1"
[99] "Pp3c1_7010V3.1" "Pp3c1_7030V3.1" "Pp3c1_7090V3.1" "Pp3c1_7160V3.1" "Pp3c1_7220V3.1" "Pp3c1_7300V3.1" "Pp3c1_7360V3.1"
[106] "Pp3c1_7370V3.1" "Pp3c1_7380V3.1" "Pp3c1_7390V3.1" "Pp3c1_7450V3.1" "Pp3c1_7500V3.1" "Pp3c1_7520V3.1" "Pp3c1_7540V3.1"
[113] "Pp3c1_7590V3.1" "Pp3c1_7710V3.1" "Pp3c1_7720V3.1" "Pp3c1_7800V3.1" "Pp3c1_7810V3.1" "Pp3c1_7830V3.1" "Pp3c1_7880V3.1"
[120] "Pp3c1_7950V3.1" "Pp3c1_8060V3.1" "Pp3c1_8080V3.1" "Pp3c1_8110V3.1" "Pp3c1_8170V3.1" "Pp3c1_8190V3.1" "Pp3c1_8210V3.1"
[127] "Pp3c1_8240V3.1" "Pp3c1_8280V3.1" "Pp3c1_8450V3.1" "Pp3c1_8490V3.1" "Pp3c1_8530V3.1" "Pp3c1_8870V3.1" "Pp3c1_8890V3.1"
[134] "Pp3c1_9180V3.1" "Pp3c1_9190V3.1" "Pp3c1_9250V3.1" "Pp3c1_9290V3.1" "Pp3c1_9320V3.1" "Pp3c1_9560V3.1" "Pp3c1_9600V3.1"
[141] "Pp3c1_9790V3.1" "Pp3c1_9860V3.1" "Pp3c1_9970V3.1" "Pp3c1_10000V3.1" "Pp3c1_10010V3.1" "Pp3c1_10040V3.1" "Pp3c1_10080V3.1"
[148] "Pp3c1_10090V3.1" "Pp3c1_10100V3.1" "Pp3c1_10220V3.1" "Pp3c1_10400V3.1" "Pp3c1_10470V3.1" "Pp3c1_10530V3.1" "Pp3c1_10540V3.1"
[155] "Pp3c1_10570V3.1" "Pp3c1_10620V3.1" "Pp3c1_10630V3.1" "Pp3c1_10810V3.1" "Pp3c1_10880V3.1" "Pp3c1_10970V3.1" "Pp3c1_11030V3.1"
[162] "Pp3c1_11050V3.1" "Pp3c1_11090V3.1" "Pp3c1_11190V3.1" "Pp3c1_11980V3.1" "Pp3c1_12020V3.1" "Pp3c1_12100V3.1" "Pp3c1_12120V3.1"
[169] "Pp3c1_12140V3.1" "Pp3c1_12470V3.1" "Pp3c1_12560V3.1" "Pp3c1_12610V3.1" "Pp3c1_12630V3.1" "Pp3c1_12730V3.1" "Pp3c1_12790V3.1"
[176] "Pp3c1_12810V3.1" "Pp3c1_12850V3.1" "Pp3c1_12860V3.1" "Pp3c1_12940V3.1" "Pp3c1_13120V3.1" "Pp3c1_13170V3.1" "Pp3c1_13270V3.1"
[183] "Pp3c1_13308V3.1" "Pp3c1_13430V3.1" "Pp3c1_13570V3.1" "Pp3c1_13640V3.1" "Pp3c1_13670V3.1" "Pp3c1_13671V3.1" "Pp3c1_13800V3.1"
[190] "Pp3c1_13830V3.1" "Pp3c1_13890V3.1" "Pp3c1_13910V3.1" "Pp3c1_13930V3.1" "Pp3c1_14230V3.1" "Pp3c1_14330V3.1" "Pp3c1_14380V3.1"
[197] "Pp3c1_14540V3.1" "Pp3c1_14740V3.1" "Pp3c1_14760V3.1" "Pp3c1_14770V3.1" "Pp3c1_14800V3.1" "Pp3c1_14870V3.1" "Pp3c1_14910V3.1"
[204] "Pp3c1_14920V3.1" "Pp3c1_14980V3.1" "Pp3c1_15010V3.1" "Pp3c1_15090V3.1" "Pp3c1_15100V3.1" "Pp3c1_15110V3.1" "Pp3c1_15150V3.1"
[211] "Pp3c1_15160V3.1" "Pp3c1_15210V3.1" "Pp3c1_15400V3.1" "Pp3c1_15410V3.1" "Pp3c1_15460V3.1" "Pp3c1_15560V3.1" "Pp3c1_15690V3.1"
[218] "Pp3c1_15730V3.1" "Pp3c1_15750V3.1" "Pp3c1_15940V3.1" "Pp3c1_16170V3.1" "Pp3c1_16250V3.1" "Pp3c1_16500V3.1" "Pp3c1_16600V3.1"
[225] "Pp3c1_16780V3.1" "Pp3c1_16840V3.1" "Pp3c1_16850V3.1" "Pp3c1_16900V3.1" "Pp3c1_16980V3.1" "Pp3c1_17080V3.1" "Pp3c1_17220V3.1"
[232] "Pp3c1_17710V3.1" "Pp3c1_17860V3.1" "Pp3c1_18050V3.1" "Pp3c1_18130V3.1" "Pp3c1_18150V3.1" "Pp3c1_18250V3.1" "Pp3c1_18260V3.1"
[239] "Pp3c1_18440V3.1" "Pp3c1_18460V3.1" "Pp3c1_18530V3.1" "Pp3c1_18680V3.1" "Pp3c1_18830V3.1" "Pp3c1_18860V3.1" "Pp3c1_18910V3.1"
[246] "Pp3c1_18940V3.1" "Pp3c1_19060V3.1" "Pp3c1_19190V3.1" "Pp3c1_19200V3.1" "Pp3c1_19210V3.1" "Pp3c1_19230V3.1" "Pp3c1_19240V3.1"
[253] "Pp3c1_19310V3.1" "Pp3c1_19370V3.1" "Pp3c1_19400V3.1" "Pp3c1_19660V3.1" "Pp3c1_19950V3.1" "Pp3c1_20100V3.1" "Pp3c1_20280V3.1"
[260] "Pp3c1_20310V3.1" "Pp3c1_20350V3.1" "Pp3c1_20430V3.1" "Pp3c1_20630V3.1" "Pp3c1_20640V3.1" "Pp3c1_20690V3.1" "Pp3c1_20700V3.1"
[267] "Pp3c1_20710V3.1" "Pp3c1_20753V3.1" "Pp3c1_20770V3.1" "Pp3c1_20790V3.1" "Pp3c1_20810V3.1" "Pp3c1_20870V3.1" "Pp3c1_20880V3.1"
[274] "Pp3c1_20960V3.1" "Pp3c1_20980V3.1" "Pp3c1_21110V3.1" "Pp3c1_21160V3.1" "Pp3c1_21200V3.1" "Pp3c1_21230V3.1" "Pp3c1_21270V3.1"
[281] "Pp3c1_21290V3.1" "Pp3c1_21480V3.1" "Pp3c1_21510V3.1" "Pp3c1_21540V3.1" "Pp3c1_21550V3.1" "Pp3c1_21620V3.1" "Pp3c1_21630V3.1"
[288] "Pp3c1_21650V3.1" "Pp3c1_21730V3.1" "Pp3c1_21760V3.1" "Pp3c1_21810V3.1" "Pp3c1_21850V3.1" "Pp3c1_21890V3.1" "Pp3c1_21920V3.1"
[295] "Pp3c1_22040V3.1" "Pp3c1_22090V3.1" "Pp3c1_22120V3.1" "Pp3c1_22240V3.1" "Pp3c1_22260V3.1" "Pp3c1_22300V3.1" "Pp3c1_22360V3.1"
[302] "Pp3c1_22450V3.1" "Pp3c1_22500V3.1" "Pp3c1_22520V3.1" "Pp3c1_22540V3.1" "Pp3c1_22560V3.1" "Pp3c1_22590V3.1" "Pp3c1_22640V3.1"
[309] "Pp3c1_22690V3.1" "Pp3c1_22710V3.1" "Pp3c1_22820V3.1" "Pp3c1_22900V3.1" "Pp3c1_22950V3.1" "Pp3c1_23010V3.1" "Pp3c1_23020V3.1"
[316] "Pp3c1_23040V3.1" "Pp3c1_23190V3.1" "Pp3c1_23260V3.1" "Pp3c1_23300V3.1" "Pp3c1_23410V3.1" "Pp3c1_23490V3.1" "Pp3c1_23590V3.1"
[323] "Pp3c1_23600V3.1" "Pp3c1_23670V3.1" "Pp3c1_23750V3.1" "Pp3c1_23850V3.1" "Pp3c1_23900V3.1" "Pp3c1_23930V3.1" "Pp3c1_23940V3.1"
[330] "Pp3c1_23960V3.1" "Pp3c1_23970V3.1" "Pp3c1_24000V3.1" "Pp3c1_24090V3.1" "Pp3c1_24120V3.1" "Pp3c1_24350V3.1" "Pp3c1_24420V3.1"
[337] "Pp3c1_24440V3.1" "Pp3c1_24500V3.1" "Pp3c1_24530V3.1" "Pp3c1_24560V3.1" "Pp3c1_24570V3.1" "Pp3c1_24600V3.1" "Pp3c1_24700V3.1"
[344] "Pp3c1_24790V3.1" "Pp3c1_24820V3.1" "Pp3c1_24950V3.1" "Pp3c1_25000V3.1" "Pp3c1_25070V3.1" "Pp3c1_25080V3.1" "Pp3c1_25290V3.1"
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[876] "Pp3c2_20120V3.1" "Pp3c2_20130V3.1" "Pp3c2_20141V3.1" "Pp3c2_20240V3.1" "Pp3c2_20320V3.1" "Pp3c2_20330V3.1" "Pp3c2_20450V3.1"
[883] "Pp3c2_20500V3.1" "Pp3c2_20550V3.1" "Pp3c2_20630V3.1" "Pp3c2_20660V3.1" "Pp3c2_20840V3.1" "Pp3c2_20860V3.1" "Pp3c2_20930V3.1"
[890] "Pp3c2_21100V3.1" "Pp3c2_21270V3.1" "Pp3c2_21290V3.1" "Pp3c2_21310V3.1" "Pp3c2_21370V3.1" "Pp3c2_21470V3.1" "Pp3c2_21580V3.1"
[897] "Pp3c2_21600V3.1" "Pp3c2_21660V3.1" "Pp3c2_21670V3.1" "Pp3c2_21710V3.1" "Pp3c2_21720V3.1" "Pp3c2_21940V3.1" "Pp3c2_21970V3.1"
[904] "Pp3c2_22000V3.1" "Pp3c2_22020V3.1" "Pp3c2_22140V3.1" "Pp3c2_22190V3.1" "Pp3c2_22570V3.1" "Pp3c2_22630V3.1" "Pp3c2_23100V3.1"
[911] "Pp3c2_23140V3.1" "Pp3c2_23200V3.1" "Pp3c2_23290V3.1" "Pp3c2_23300V3.1" "Pp3c2_23320V3.1" "Pp3c2_23750V3.1" "Pp3c2_23860V3.1"
[918] "Pp3c2_23870V3.1" "Pp3c2_23900V3.1" "Pp3c2_24110V3.1" "Pp3c2_24130V3.1" "Pp3c2_24150V3.1" "Pp3c2_24160V3.1" "Pp3c2_24230V3.1"
[925] "Pp3c2_24270V3.1" "Pp3c2_24500V3.1" "Pp3c2_24620V3.1" "Pp3c2_24640V3.1" "Pp3c2_24670V3.1" "Pp3c2_24723V3.1" "Pp3c2_24761V3.1"
[932] "Pp3c2_24840V3.1" "Pp3c2_24870V3.1" "Pp3c2_24910V3.1" "Pp3c2_25000V3.1" "Pp3c2_25170V3.1" "Pp3c2_25440V3.1" "Pp3c2_25580V3.1"
[939] "Pp3c2_25690V3.1" "Pp3c2_25760V3.1" "Pp3c2_25890V3.1" "Pp3c2_25930V3.1" "Pp3c2_26060V3.1" "Pp3c2_26200V3.1" "Pp3c2_26250V3.1"
[946] "Pp3c2_26270V3.1" "Pp3c2_26320V3.1" "Pp3c2_26540V3.1" "Pp3c2_26650V3.1" "Pp3c2_26700V3.1" "Pp3c2_26720V3.1" "Pp3c2_26890V3.1"
[953] "Pp3c2_27120V3.1" "Pp3c2_27180V3.1" "Pp3c2_27270V3.1" "Pp3c2_27310V3.1" "Pp3c2_27320V3.1" "Pp3c2_27330V3.1" "Pp3c2_27340V3.1"
[960] "Pp3c2_27350V3.1" "Pp3c2_27440V3.1" "Pp3c2_27510V3.1" "Pp3c2_27540V3.1" "Pp3c2_27550V3.1" "Pp3c2_27590V3.1" "Pp3c2_27820V3.1"
[967] "Pp3c2_27880V3.1" "Pp3c2_27910V3.1" "Pp3c2_27940V3.1" "Pp3c2_27980V3.1" "Pp3c2_28010V3.1" "Pp3c2_28030V3.1" "Pp3c2_28040V3.1"
[974] "Pp3c2_28070V3.1" "Pp3c2_28130V3.1" "Pp3c2_28140V3.1" "Pp3c2_28180V3.1" "Pp3c2_28280V3.1" "Pp3c2_28380V3.1" "Pp3c2_28420V3.1"
[981] "Pp3c2_28540V3.1" "Pp3c2_28550V3.1" "Pp3c2_28570V3.1" "Pp3c2_28690V3.1" "Pp3c2_28870V3.1" "Pp3c2_28950V3.1" "Pp3c2_29040V3.1"
[988] "Pp3c2_29090V3.1" "Pp3c2_29140V3.1" "Pp3c2_29249V3.1" "Pp3c2_29290V3.1" "Pp3c2_29420V3.1" "Pp3c2_29500V3.1" "Pp3c2_29560V3.1"
[995] "Pp3c2_29570V3.1" "Pp3c2_29720V3.1" "Pp3c2_29800V3.1" "Pp3c2_29840V3.1" "Pp3c2_29920V3.1" "Pp3c2_30010V3.1"
[ reached getOption("max.print") -- omitted 7578 entries ]
runs/RNA-Seq_analysis/DEGs/DEGs_0.9/cop_D_cop_L/DESeq2/cop_D vs. cop_L_12443_DESeq2_fdr.tsv 0 → 100755
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runs/RNA-Seq_analysis/DEGs/DEGs_0.9/cop_D_cop_L/NOISeq/cop_D vs. cop_L_10103_NOISeqbio_tmm_prob_seed_12345.tsv 0 → 100755
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