Summary: The gene counts table was normalized for inherent systematic or experimental biases (e.g. sequencing depth, gene length, GC content bias etc.) using the Bioconductor package DESeq after removing genes that had zero counts over all the RNA-Seq samples (17090 genes). The output of the normalization algorithm was a table with normalized counts, which can be used for differential expression analysis with statistical algorithms developed specifically for count data. Prior to the statistical testing procedure, the gene read counts were filtered for possible artifacts that could affect the subsequent statistical testing procedures. Genes presenting any of the following were excluded from further analysis: i) genes with length less than 500 (5628 genes), ii) genes whose average reads per 100 bp was less than the 25^th quantile of the total normalized distribution of average reads per 100bp (0 genes with cutoff value 0 average reads per 100 bp), iii) genes with read counts below the median read counts of the total normalized count distribution (6972 genes with cutoff value 1 normalized read counts), iv) genes whose biotype matched the following: rRNA, IG_V_pseudogene, TR_V_pseudogene (170 genes). The total number of genes excluded due to the application of gene filters was 5799. The total (unified) number of genes excluded due to the application of all filters was 27684. The resulting gene counts table was subjected to differential expression analysis for the contrasts group1 versus group3, group2 versus group4, group3 versus group5, group3 versus group7, group3 versus group13, group5 versus group7, group5 versus group13, group6 versus group8, group7 versus group13, group15 versus group16, group13 versus group15 using the Bioconductor packages DESeq, edgeR, limma, NBPSeq, NOISeq. In order to combine the statistical significance from multiple algorithms and perform meta-analysis, the PANDORA weighted p-value across results method was applied. The final numbers of differentially expressed genes were (per contrast): for the contrast group1 versus group3, 189 (0) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 155 were up-regulated, 27 were down-regulated and 7 were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast group2 versus group4, 1017 (1) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 529 (1) were up-regulated, 273 (0) were down-regulated and 215 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast group3 versus group5, 1245 (150) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 460 (23) were up-regulated, 661 (127) were down-regulated and 124 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast group3 versus group7, 830 (2) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 503 (2) were up-regulated, 228 (0) were down-regulated and 99 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast group3 versus group13, 972 (15) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 264 (2) were up-regulated, 679 (13) were down-regulated and 29 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast group5 versus group7, 1232 (127) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 891 (125) were up-regulated, 202 (2) were down-regulated and 139 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast group5 versus group13, 796 (6) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 258 (3) were up-regulated, 437 (3) were down-regulated and 101 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast group6 versus group8, 1307 (165) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 768 (159) were up-regulated, 365 (6) were down-regulated and 174 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast group7 versus group13, 1442 (11) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 215 (0) were up-regulated, 1158 (11) were down-regulated and 69 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast group15 versus group16, 345 (0) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 185 were up-regulated, 119 were down-regulated and 41 were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast group13 versus group15, 653 (0) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 487 were up-regulated, 125 were down-regulated and 41 were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale. Literature references for all the algorithms used can be found at the end of this report.

Read counts file: imported custom data frame
Conditions: group1, group2, group3, group4, group5, group6, group7, group8, group9, group10, group11, group12, group13, group14, group15, group16
Samples included: 1_k7_T1, 3_k8_T1, 15_k5_T_o-n, 17_k6_T_o-n, 2_k7_T1_plusTNF5, 4_k8_T1_plusTNF5, 16_k5_T_o-n_plusTNF5, 18_k6_T_o-n_plusTNF5, 9_k7_D, 11_k8_D, 23_k6_D, 10_k7_D_plusTNF5, 12_k8_D_plusTNF5, 24_k6_D_plusTNF5, 5_Tgk7_T1, 7_Tgk8_T1, 19_Tgk5_T_o-n, 21_Tgk6_T_o-n, 6_k7_T1_plusTNF5, 8_Tgk8_T1_plusTNF5, 20_Tgk5_T_o-n_plusTNF5, 22_Tgk6_T_o-n_plusTNF5, 13_Tgk8_D, 25_Tgk5_D, 27_Tgk6_D, 14_k8_D_plusTNF5, 26_Tgk5_D_plusTNF5, 28_Tgk6_D_plusTNF5, 29_TgKR1_T1, 31_TgK22_0h, 30_gKR1_T1_plusTNF5, 32_TgK22_5h, 37_TgKR1_D, 41_TgKR1_P, 38_TgKR1_D_plusTNF5, 42_TgKR1_P_plusTNF5, 33_TgK23_0h, 35_TgKR2_T2, 34_TgK23_5h, 36_TgKR2_T2_plusTNF5, 39_TgKR2_D, 43_TgKR2_P, 40_TgKR2_D_plusTNF5, 44_TgKR2P_plusTNF5
Samples excluded: none
Requested contrasts: group1_vs_group3, group2_vs_group4, group3_vs_group5, group3_vs_group7, group3_vs_group13, group5_vs_group7, group5_vs_group13, group6_vs_group8, group7_vs_group13, group15_vs_group16, group13_vs_group15
Library sizes: not available
Annotation: embedded
Organism:
Annotation source: Ensembl genomes
Count type: utr
3' UTR flanking :: 500
Exon filters: none applied
Gene filters: length, avg.reads, expression, biotype

• length
  • length: 500

• avg.reads
  • average.per.bp: 100
  • quantile: 0.25

• expression
  • median: TRUE
  • mean: FALSE
  • quantile: NA
  • known: NA
  • custom: NA

• biotype
  • pseudogene: FALSE
  • snRNA: FALSE
  • protein_coding: FALSE
  • antisense: FALSE
  • miRNA: FALSE
  • snoRNA: FALSE
  • lincRNA: FALSE
  • processed_transcript: FALSE
  • misc_RNA: FALSE
  • rRNA: TRUE
  • sense_intronic: FALSE
  • sense_overlapping: FALSE
  • polymorphic_pseudogene: FALSE
  • IG_C_gene: FALSE
  • IG_J_gene: FALSE
  • IG_D_gene: FALSE
  • IG_LV_gene: FALSE
  • IG_V_gene: FALSE
  • IG_V_pseudogene: TRUE
  • TR_V_gene: FALSE
  • TR_V_pseudogene: TRUE
  • three_prime_overlapping_ncrna: FALSE

Filter application: after normalization
Normalization algorithm: DESeq
Normalization arguments: locfunc

• [[list(locfunc = function (x, na.rm = FALSE, ...) standardGeneric("median"))locfunc

Statistical algorithm(s): DESeq, edgeR, limma, NBPSeq, NOISeq
Statistical arguments for DESeq: method, sharingMode, fitType

• method: blind
• sharingMode: fit-only
• fitType: local

Statistical arguments for edgeR: main.method, rowsum.filter, prior.df, trend, span, tag.method, grid.length, grid.range, offset, glm.method, subset, AveLogCPM, trend.method, dispersion, offset, weights, lib.size, prior.count, start, method, test, abundance.trend, robust, winsor.tail.p

• main.method: classic
• rowsum.filter: 5
• prior.df: 10
• trend: movingave
• tag.method: grid
• grid.length: 11
• grid.range: -6, 6
• glm.method: CoxReid
• subset: 10000
• trend.method: auto
• prior.count: 0.125
• method: auto
• test: chisq
• abundance.trend: TRUE
• robust: FALSE
• winsor.tail.p: 0.05, 0.1

Statistical arguments for limma: normalize.method

• normalize.method: none

Statistical arguments for NBPSeq: main.method, model, tests, alternative

• main.method: nbsmyth
• model: log-linear-rel-mean, NBP
• tests: HOA
• alternative: two.sided

Statistical arguments for NOISeq: k, norm, replicates, factor, conditions, pnr, nss, v, lc, nclust, r, adj, a0per, filter, depth, cv.cutoff, cpm

• k: 0.5
• norm: n
• replicates: biological
• factor: class
• pnr: 0.2
• nss: 5
• v: 0.02
• lc: 1
• nclust: 15
• r: 100
• adj: 1.5
• a0per: 0.9
• filter: 0
• cv.cutoff: 500
• cpm: 1

Meta-analysis method: PANDORA weighted p-value across results
Multiple testing correction: Benjamini-Hochberg FDR
p-value threshold: 0.05
Logarithmic tranformation offset: 1
Analysis preset: not available
Quality control plots: multidimensional scaling, biotype detection, biotype counts, sample and biotype saturation, filtered biotypes, correlation heatmap and correlogram, boxplots, GC-content bias, transcript length bias, mean-difference plot, mean-variance plot, DEG biotype detection, volcano plot, DEG heatmap
Figure format: png, pdf
Output directory: ~/GKlab/run_303_pandora/metaseqr_quantseq_run303_pandora_new_contrasts
Output data: Annotation, p-value, Adjusted p-value (FDR), Fold change, Statistics, Read counts
Output scale(s): Natural scale, log2 scale, Reads per Gene Model
Output values: Normalized values
Output statistics: Mean
Total run time: 01 hours 31 minutes 11 seconds

Number of filtered genes: 27684 which is the union of

• Filtered because of zero reads: 17090
• Filtered because of exon filters: 0
• Filtered because of gene filters: 10594 which is the union of
  • length: 5628 genes with filter cutoff value 500
  • avg.reads: 0 genes with filter cutoff value 0
  • expression: 6972 genes further decomposed to (filter name, filtered genes, filter cutoff):
  • • median: 6972 genes with filter cutoff value 1
  • biotype: 170 genes with filter cutoff value rRNA, IG_V_pseudogene, TR_V_pseudogene

Number of differentially expressed genes per contrast:

• group1_vs_group3: 189 (0) statistically significant genes of which 155 up regulated, 27 down regulated and 7 not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale. These numbers refer to the combined analysis performed by metaseqR. Per statistical algorithm, the differentially expressed genes are:
  • DESeq: 52 (0) statistically significant genes of which 39 (0) up regulated, 12 (0) down regulated and 1 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • edgeR: 247 (0) statistically significant genes of which 183 (0) up regulated, 48 (0) down regulated and 16 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • limma: 303 (0) statistically significant genes of which 215 (0) up regulated, 60 (0) down regulated and 28 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NBPSeq: 437 (17) statistically significant genes of which 334 (16) up regulated, 96 (1) down regulated and 7 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NOISeq: 4 (2) statistically significant genes of which 1 (0) up regulated, 0 (0) down regulated and 3 (2) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• group2_vs_group4: 1017 (1) statistically significant genes of which 529 (1) up regulated, 273 (0) down regulated and 215 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale. These numbers refer to the combined analysis performed by metaseqR. Per statistical algorithm, the differentially expressed genes are:
  • DESeq: 520 (24) statistically significant genes of which 446 (20) up regulated, 74 (4) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • edgeR: 867 (20) statistically significant genes of which 545 (15) up regulated, 202 (5) down regulated and 120 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • limma: 1795 (0) statistically significant genes of which 609 (0) up regulated, 429 (0) down regulated and 757 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NBPSeq: 1382 (326) statistically significant genes of which 1135 (291) up regulated, 237 (35) down regulated and 10 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NOISeq: 1112 (70) statistically significant genes of which 666 (5) up regulated, 162 (54) down regulated and 284 (11) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• group3_vs_group5: 1245 (150) statistically significant genes of which 460 (23) up regulated, 661 (127) down regulated and 124 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale. These numbers refer to the combined analysis performed by metaseqR. Per statistical algorithm, the differentially expressed genes are:
  • DESeq: 587 (107) statistically significant genes of which 142 (8) up regulated, 443 (99) down regulated and 2 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • edgeR: 1205 (234) statistically significant genes of which 414 (44) up regulated, 668 (190) down regulated and 123 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • limma: 1819 (61) statistically significant genes of which 615 (9) up regulated, 785 (52) down regulated and 419 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NBPSeq: 1286 (303) statistically significant genes of which 451 (57) up regulated, 828 (246) down regulated and 7 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NOISeq: 642 (131) statistically significant genes of which 234 (30) up regulated, 293 (93) down regulated and 115 (8) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• group3_vs_group7: 830 (2) statistically significant genes of which 503 (2) up regulated, 228 (0) down regulated and 99 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale. These numbers refer to the combined analysis performed by metaseqR. Per statistical algorithm, the differentially expressed genes are:
  • DESeq: 465 (15) statistically significant genes of which 377 (11) up regulated, 88 (4) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • edgeR: 935 (12) statistically significant genes of which 565 (9) up regulated, 243 (3) down regulated and 127 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • limma: 952 (0) statistically significant genes of which 490 (0) up regulated, 251 (0) down regulated and 211 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NBPSeq: 1380 (241) statistically significant genes of which 1182 (216) up regulated, 190 (25) down regulated and 8 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NOISeq: 2023 (9) statistically significant genes of which 1561 (8) up regulated, 48 (1) down regulated and 414 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• group3_vs_group13: 972 (15) statistically significant genes of which 264 (2) up regulated, 679 (13) down regulated and 29 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale. These numbers refer to the combined analysis performed by metaseqR. Per statistical algorithm, the differentially expressed genes are:
  • DESeq: 557 (130) statistically significant genes of which 74 (6) up regulated, 483 (124) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • edgeR: 860 (50) statistically significant genes of which 250 (13) up regulated, 572 (37) down regulated and 38 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • limma: 1101 (0) statistically significant genes of which 365 (0) up regulated, 608 (0) down regulated and 128 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NBPSeq: 1176 (275) statistically significant genes of which 372 (20) up regulated, 802 (255) down regulated and 2 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NOISeq: 543 (134) statistically significant genes of which 49 (6) up regulated, 445 (120) down regulated and 49 (8) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• group5_vs_group7: 1232 (127) statistically significant genes of which 891 (125) up regulated, 202 (2) down regulated and 139 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale. These numbers refer to the combined analysis performed by metaseqR. Per statistical algorithm, the differentially expressed genes are:
  • DESeq: 923 (214) statistically significant genes of which 875 (212) up regulated, 47 (2) down regulated and 1 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • edgeR: 1180 (181) statistically significant genes of which 872 (171) up regulated, 180 (10) down regulated and 128 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • limma: 1599 (80) statistically significant genes of which 835 (78) up regulated, 296 (2) down regulated and 468 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NBPSeq: 1727 (787) statistically significant genes of which 1564 (765) up regulated, 149 (22) down regulated and 14 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NOISeq: 1539 (94) statistically significant genes of which 1201 (76) up regulated, 57 (9) down regulated and 281 (9) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• group5_vs_group13: 796 (6) statistically significant genes of which 258 (3) up regulated, 437 (3) down regulated and 101 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale. These numbers refer to the combined analysis performed by metaseqR. Per statistical algorithm, the differentially expressed genes are:
  • DESeq: 363 (108) statistically significant genes of which 93 (22) up regulated, 270 (86) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • edgeR: 423 (17) statistically significant genes of which 190 (13) up regulated, 220 (4) down regulated and 13 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • limma: 1431 (0) statistically significant genes of which 301 (0) up regulated, 631 (0) down regulated and 499 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NBPSeq: 746 (144) statistically significant genes of which 253 (36) up regulated, 470 (108) down regulated and 23 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NOISeq: 611 (98) statistically significant genes of which 44 (13) up regulated, 382 (52) down regulated and 185 (33) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• group6_vs_group8: 1307 (165) statistically significant genes of which 768 (159) up regulated, 365 (6) down regulated and 174 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale. These numbers refer to the combined analysis performed by metaseqR. Per statistical algorithm, the differentially expressed genes are:
  • DESeq: 747 (229) statistically significant genes of which 376 (115) up regulated, 371 (114) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • edgeR: 1170 (214) statistically significant genes of which 717 (206) up regulated, 268 (8) down regulated and 185 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • limma: 1941 (172) statistically significant genes of which 932 (154) up regulated, 445 (18) down regulated and 564 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NBPSeq: 1277 (403) statistically significant genes of which 666 (230) up regulated, 603 (173) down regulated and 8 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NOISeq: 650 (149) statistically significant genes of which 269 (118) up regulated, 265 (21) down regulated and 116 (10) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• group7_vs_group13: 1442 (11) statistically significant genes of which 215 (0) up regulated, 1158 (11) down regulated and 69 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale. These numbers refer to the combined analysis performed by metaseqR. Per statistical algorithm, the differentially expressed genes are:
  • DESeq: 824 (220) statistically significant genes of which 30 (1) up regulated, 794 (219) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • edgeR: 1099 (17) statistically significant genes of which 183 (2) up regulated, 894 (15) down regulated and 22 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • limma: 1541 (0) statistically significant genes of which 316 (0) up regulated, 1023 (0) down regulated and 202 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NBPSeq: 1681 (580) statistically significant genes of which 199 (16) up regulated, 1480 (564) down regulated and 2 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NOISeq: 9910 (299) statistically significant genes of which 794 (25) up regulated, 4642 (235) down regulated and 4474 (39) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• group15_vs_group16: 345 (0) statistically significant genes of which 185 up regulated, 119 down regulated and 41 not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale. These numbers refer to the combined analysis performed by metaseqR. Per statistical algorithm, the differentially expressed genes are:
  • DESeq: 25 (0) statistically significant genes of which 15 (0) up regulated, 10 (0) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • edgeR: 142 (0) statistically significant genes of which 66 (0) up regulated, 76 (0) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • limma: 1367 (0) statistically significant genes of which 630 (0) up regulated, 292 (0) down regulated and 445 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NBPSeq: 127 (0) statistically significant genes of which 71 (0) up regulated, 56 (0) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NOISeq: 60 (27) statistically significant genes of which 23 (12) up regulated, 3 (1) down regulated and 34 (14) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• group13_vs_group15: 653 (0) statistically significant genes of which 487 up regulated, 125 down regulated and 41 not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale. These numbers refer to the combined analysis performed by metaseqR. Per statistical algorithm, the differentially expressed genes are:
  • DESeq: 180 (4) statistically significant genes of which 173 (4) up regulated, 7 (0) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • edgeR: 538 (7) statistically significant genes of which 427 (7) up regulated, 105 (0) down regulated and 6 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • limma: 1514 (0) statistically significant genes of which 803 (0) up regulated, 382 (0) down regulated and 329 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NBPSeq: 560 (22) statistically significant genes of which 493 (22) up regulated, 67 (0) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
  • NOISeq: 420 (94) statistically significant genes of which 293 (73) up regulated, 20 (3) down regulated and 107 (18) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.

[ 2018-08-03 15:49:51 ] INFO 2018-08-03 15:49:51: Data processing started...
[ 2018-08-03 15:49:51 ] INFO Read counts file: imported custom data frame
[ 2018-08-03 15:49:51 ] INFO Conditions: group1, group2, group3, group4, group5, group6, group7, group8, group9, group10, group11, group12, group13, group14, group15, group16
[ 2018-08-03 15:49:51 ] INFO Samples to include: 1_k7_T1, 3_k8_T1, 15_k5_T_o-n, 17_k6_T_o-n, 2_k7_T1_plusTNF5, 4_k8_T1_plusTNF5, 16_k5_T_o-n_plusTNF5, 18_k6_T_o-n_plusTNF5, 9_k7_D, 11_k8_D, 23_k6_D, 10_k7_D_plusTNF5, 12_k8_D_plusTNF5, 24_k6_D_plusTNF5, 5_Tgk7_T1, 7_Tgk8_T1, 19_Tgk5_T_o-n, 21_Tgk6_T_o-n, 6_k7_T1_plusTNF5, 8_Tgk8_T1_plusTNF5, 20_Tgk5_T_o-n_plusTNF5, 22_Tgk6_T_o-n_plusTNF5, 13_Tgk8_D, 25_Tgk5_D, 27_Tgk6_D, 14_k8_D_plusTNF5, 26_Tgk5_D_plusTNF5, 28_Tgk6_D_plusTNF5, 29_TgKR1_T1, 31_TgK22_0h, 30_gKR1_T1_plusTNF5, 32_TgK22_5h, 37_TgKR1_D, 41_TgKR1_P, 38_TgKR1_D_plusTNF5, 42_TgKR1_P_plusTNF5, 33_TgK23_0h, 35_TgKR2_T2, 34_TgK23_5h, 36_TgKR2_T2_plusTNF5, 39_TgKR2_D, 43_TgKR2_P, 40_TgKR2_D_plusTNF5, 44_TgKR2P_plusTNF5
[ 2018-08-03 15:49:51 ] INFO Samples to exclude: none
[ 2018-08-03 15:49:51 ] INFO Requested contrasts: group1_vs_group3, group2_vs_group4, group3_vs_group5, group3_vs_group7, group3_vs_group13, group5_vs_group7, group5_vs_group13, group6_vs_group8, group7_vs_group13, group15_vs_group16, group13_vs_group15
[ 2018-08-03 15:49:51 ] INFO Annotation: embedded
[ 2018-08-03 15:49:51 ] INFO Organism: custom
[ 2018-08-03 15:49:51 ] INFO Reference source: ensembl
[ 2018-08-03 15:49:51 ] INFO Count type: utr
[ 2018-08-03 15:49:51 ] INFO 3' UTR flanking: 500
[ 2018-08-03 15:49:51 ] INFO Exon filters: none applied
[ 2018-08-03 15:49:51 ] INFO Gene filters: length, avg.reads, expression, biotype
[ 2018-08-03 15:49:51 ] INFO length:
[ 2018-08-03 15:49:51 ] INFO length: 500
[ 2018-08-03 15:49:51 ] INFO avg.reads:
[ 2018-08-03 15:49:51 ] INFO average.per.bp: 100
[ 2018-08-03 15:49:51 ] INFO quantile: 0.25
[ 2018-08-03 15:49:51 ] INFO expression:
[ 2018-08-03 15:49:51 ] INFO median: TRUE
[ 2018-08-03 15:49:51 ] INFO mean: FALSE
[ 2018-08-03 15:49:51 ] INFO quantile: NA
[ 2018-08-03 15:49:51 ] INFO known: NA
[ 2018-08-03 15:49:51 ] INFO custom: NA
[ 2018-08-03 15:49:51 ] INFO biotype:
[ 2018-08-03 15:49:51 ] INFO pseudogene: FALSE
[ 2018-08-03 15:49:51 ] INFO snRNA: FALSE
[ 2018-08-03 15:49:51 ] INFO protein_coding: FALSE
[ 2018-08-03 15:49:51 ] INFO antisense: FALSE
[ 2018-08-03 15:49:51 ] INFO miRNA: FALSE
[ 2018-08-03 15:49:51 ] INFO snoRNA: FALSE
[ 2018-08-03 15:49:51 ] INFO lincRNA: FALSE
[ 2018-08-03 15:49:51 ] INFO processed_transcript: FALSE
[ 2018-08-03 15:49:51 ] INFO misc_RNA: FALSE
[ 2018-08-03 15:49:51 ] INFO rRNA: TRUE
[ 2018-08-03 15:49:51 ] INFO sense_intronic: FALSE
[ 2018-08-03 15:49:51 ] INFO sense_overlapping: FALSE
[ 2018-08-03 15:49:51 ] INFO polymorphic_pseudogene: FALSE
[ 2018-08-03 15:49:51 ] INFO IG_C_gene: FALSE
[ 2018-08-03 15:49:51 ] INFO IG_J_gene: FALSE
[ 2018-08-03 15:49:51 ] INFO IG_D_gene: FALSE
[ 2018-08-03 15:49:51 ] INFO IG_LV_gene: FALSE
[ 2018-08-03 15:49:51 ] INFO IG_V_gene: FALSE
[ 2018-08-03 15:49:51 ] INFO IG_V_pseudogene: TRUE
[ 2018-08-03 15:49:51 ] INFO TR_V_gene: FALSE
[ 2018-08-03 15:49:51 ] INFO TR_V_pseudogene: TRUE
[ 2018-08-03 15:49:51 ] INFO three_prime_overlapping_ncrna: FALSE
[ 2018-08-03 15:49:51 ] INFO Filter application: postnorm
[ 2018-08-03 15:49:51 ] INFO Normalization algorithm: deseq
[ 2018-08-03 15:49:51 ] INFO Normalization arguments:
[ 2018-08-03 15:49:51 ] INFO locfunc:
[ 2018-08-03 15:49:51 ] INFO [[
[ 2018-08-03 15:49:51 ] INFO list(locfunc = function (x, na.rm = FALSE, ...) standardGeneric("median"))
[ 2018-08-03 15:49:51 ] INFO locfunc
[ 2018-08-03 15:49:51 ] INFO Statistical algorithm: deseq, edger, limma, nbpseq, noiseq
[ 2018-08-03 15:49:51 ] INFO Statistical arguments:
[ 2018-08-03 15:49:51 ] INFO deseq: blind, fit-only, local
[ 2018-08-03 15:49:51 ] INFO edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
[ 2018-08-03 15:49:51 ] INFO limma: none
[ 2018-08-03 15:49:51 ] INFO nbpseq: nbsmyth, list(nbpseq = "log-linear-rel-mean", nbsmyth = "NBP"), HOA, two.sided
[ 2018-08-03 15:49:51 ] INFO noiseq: 0.5, n, biological, class, NULL, 0.2, 5, 0.02, 1, 15, 100, 1.5, 0.9, 0, NULL, 500, 1
[ 2018-08-03 15:49:51 ] INFO Meta-analysis method: pandora
[ 2018-08-03 15:49:51 ] INFO Multiple testing correction: BH
[ 2018-08-03 15:49:51 ] INFO p-value threshold: 0.05
[ 2018-08-03 15:49:51 ] INFO Logarithmic transformation offset: 1
[ 2018-08-03 15:49:51 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap
[ 2018-08-03 15:49:51 ] INFO Figure format: png, pdf
[ 2018-08-03 15:49:51 ] INFO Output directory: ~/GKlab/run_303_pandora/metaseqr_quantseq_run303_pandora_new_contrasts
[ 2018-08-03 15:49:51 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, meta.p.value, adj.meta.p.value, stats, counts, flags
[ 2018-08-03 15:49:51 ] INFO Output scale(s): natural, log2, rpgm
[ 2018-08-03 15:49:51 ] INFO Output values: normalized
[ 2018-08-03 15:49:51 ] INFO Output statistics: mean
[ 2018-08-03 15:49:51 ] INFO Reading custom external gene annotation for from /data/results/tools/rnaseq/metaseqr/mm10/gene_data_mm10.txt.gz...
[ 2018-08-03 15:49:53 ] INFO Checking chromosomes in transcript counts and gene annotation...
[ 2018-08-03 15:49:53 ] INFO Processing transcripts...
[ 2018-08-03 15:49:53 ] INFO Separating transcripts (UTR regions) per gene for 1_k7_T1...
[ 2018-08-03 15:50:47 ] INFO Separating transcripts (UTR regions) per gene for 3_k8_T1...
[ 2018-08-03 15:51:42 ] INFO Separating transcripts (UTR regions) per gene for 15_k5_T_o-n...
[ 2018-08-03 15:52:37 ] INFO Separating transcripts (UTR regions) per gene for 17_k6_T_o-n...
[ 2018-08-03 15:53:31 ] INFO Separating transcripts (UTR regions) per gene for 2_k7_T1_plusTNF5...
[ 2018-08-03 15:54:28 ] INFO Separating transcripts (UTR regions) per gene for 4_k8_T1_plusTNF5...
[ 2018-08-03 15:55:25 ] INFO Separating transcripts (UTR regions) per gene for 16_k5_T_o-n_plusTNF5...
[ 2018-08-03 15:56:22 ] INFO Separating transcripts (UTR regions) per gene for 18_k6_T_o-n_plusTNF5...
[ 2018-08-03 15:57:20 ] INFO Separating transcripts (UTR regions) per gene for 9_k7_D...
[ 2018-08-03 15:58:17 ] INFO Separating transcripts (UTR regions) per gene for 11_k8_D...
[ 2018-08-03 15:59:14 ] INFO Separating transcripts (UTR regions) per gene for 23_k6_D...
[ 2018-08-03 16:00:13 ] INFO Separating transcripts (UTR regions) per gene for 10_k7_D_plusTNF5...
[ 2018-08-03 16:01:11 ] INFO Separating transcripts (UTR regions) per gene for 12_k8_D_plusTNF5...
[ 2018-08-03 16:02:10 ] INFO Separating transcripts (UTR regions) per gene for 24_k6_D_plusTNF5...
[ 2018-08-03 16:03:09 ] INFO Separating transcripts (UTR regions) per gene for 5_Tgk7_T1...
[ 2018-08-03 16:04:07 ] INFO Separating transcripts (UTR regions) per gene for 7_Tgk8_T1...
[ 2018-08-03 16:05:07 ] INFO Separating transcripts (UTR regions) per gene for 19_Tgk5_T_o-n...
[ 2018-08-03 16:06:06 ] INFO Separating transcripts (UTR regions) per gene for 21_Tgk6_T_o-n...
[ 2018-08-03 16:07:06 ] INFO Separating transcripts (UTR regions) per gene for 6_k7_T1_plusTNF5...
[ 2018-08-03 16:08:05 ] INFO Separating transcripts (UTR regions) per gene for 8_Tgk8_T1_plusTNF5...
[ 2018-08-03 16:09:04 ] INFO Separating transcripts (UTR regions) per gene for 20_Tgk5_T_o-n_plusTNF5...
[ 2018-08-03 16:10:05 ] INFO Separating transcripts (UTR regions) per gene for 22_Tgk6_T_o-n_plusTNF5...
[ 2018-08-03 16:11:05 ] INFO Separating transcripts (UTR regions) per gene for 13_Tgk8_D...
[ 2018-08-03 16:12:02 ] INFO Separating transcripts (UTR regions) per gene for 25_Tgk5_D...
[ 2018-08-03 16:12:59 ] INFO Separating transcripts (UTR regions) per gene for 27_Tgk6_D...
[ 2018-08-03 16:13:56 ] INFO Separating transcripts (UTR regions) per gene for 14_k8_D_plusTNF5...
[ 2018-08-03 16:14:55 ] INFO Separating transcripts (UTR regions) per gene for 26_Tgk5_D_plusTNF5...
[ 2018-08-03 16:15:55 ] INFO Separating transcripts (UTR regions) per gene for 28_Tgk6_D_plusTNF5...
[ 2018-08-03 16:16:54 ] INFO Separating transcripts (UTR regions) per gene for 29_TgKR1_T1...
[ 2018-08-03 16:17:52 ] INFO Separating transcripts (UTR regions) per gene for 31_TgK22_0h...
[ 2018-08-03 16:18:51 ] INFO Separating transcripts (UTR regions) per gene for 30_gKR1_T1_plusTNF5...
[ 2018-08-03 16:19:50 ] INFO Separating transcripts (UTR regions) per gene for 32_TgK22_5h...
[ 2018-08-03 16:20:49 ] INFO Separating transcripts (UTR regions) per gene for 37_TgKR1_D...
[ 2018-08-03 16:21:48 ] INFO Separating transcripts (UTR regions) per gene for 41_TgKR1_P...
[ 2018-08-03 16:22:48 ] INFO Separating transcripts (UTR regions) per gene for 38_TgKR1_D_plusTNF5...
[ 2018-08-03 16:23:46 ] INFO Separating transcripts (UTR regions) per gene for 42_TgKR1_P_plusTNF5...
[ 2018-08-03 16:24:46 ] INFO Separating transcripts (UTR regions) per gene for 33_TgK23_0h...
[ 2018-08-03 16:25:43 ] INFO Separating transcripts (UTR regions) per gene for 35_TgKR2_T2...
[ 2018-08-03 16:26:40 ] INFO Separating transcripts (UTR regions) per gene for 34_TgK23_5h...
[ 2018-08-03 16:27:39 ] INFO Separating transcripts (UTR regions) per gene for 36_TgKR2_T2_plusTNF5...
[ 2018-08-03 16:28:37 ] INFO Separating transcripts (UTR regions) per gene for 39_TgKR2_D...
[ 2018-08-03 16:29:36 ] INFO Separating transcripts (UTR regions) per gene for 43_TgKR2_P...
[ 2018-08-03 16:30:35 ] INFO Separating transcripts (UTR regions) per gene for 40_TgKR2_D_plusTNF5...
[ 2018-08-03 16:31:34 ] INFO Separating transcripts (UTR regions) per gene for 44_TgKR2P_plusTNF5...
[ 2018-08-03 16:32:33 ] INFO Saving gene model to ~/GKlab/run_303_pandora/metaseqr_quantseq_run303_pandora_new_contrasts/data/gene_model.RData
[ 2018-08-03 16:32:42 ] INFO Summarizing count data...
[ 2018-08-03 16:33:10 ] INFO Removing genes with zero counts in all samples...
[ 2018-08-03 16:33:11 ] INFO Normalizing with: deseq
[ 2018-08-03 16:33:12 ] INFO Applying gene filter length...
[ 2018-08-03 16:33:12 ] INFO Threshold below which ignored: 500
[ 2018-08-03 16:33:12 ] INFO Applying gene filter avg.reads...
[ 2018-08-03 16:33:12 ] INFO Threshold below which ignored: 0
[ 2018-08-03 16:33:12 ] INFO Applying gene filter expression...
[ 2018-08-03 16:33:12 ] INFO Threshold below which ignored: 1
[ 2018-08-03 16:33:12 ] INFO Applying gene filter biotype...
[ 2018-08-03 16:33:12 ] INFO Biotypes ignored: rRNA, IG_V_pseudogene, TR_V_pseudogene
[ 2018-08-03 16:33:13 ] INFO 27684 genes filtered out
[ 2018-08-03 16:33:13 ] INFO 21864 genes remain after filtering
[ 2018-08-03 16:33:13 ] INFO Running statistical tests with: deseq
[ 2018-08-03 16:33:14 ] INFO Contrast: group1_vs_group3
[ 2018-08-03 16:33:30 ] INFO Contrast: group2_vs_group4
[ 2018-08-03 16:33:46 ] INFO Contrast: group3_vs_group5
[ 2018-08-03 16:34:05 ] INFO Contrast: group3_vs_group7
[ 2018-08-03 16:34:20 ] INFO Contrast: group3_vs_group13
[ 2018-08-03 16:34:33 ] INFO Contrast: group5_vs_group7
[ 2018-08-03 16:34:51 ] INFO Contrast: group5_vs_group13
[ 2018-08-03 16:35:08 ] INFO Contrast: group6_vs_group8
[ 2018-08-03 16:35:26 ] INFO Contrast: group7_vs_group13
[ 2018-08-03 16:35:38 ] INFO Contrast: group15_vs_group16
[ 2018-08-03 16:35:51 ] INFO Contrast: group13_vs_group15
[ 2018-08-03 16:36:01 ] INFO Contrast group1_vs_group3: found 52 genes
[ 2018-08-03 16:36:01 ] INFO Contrast group2_vs_group4: found 520 genes
[ 2018-08-03 16:36:01 ] INFO Contrast group3_vs_group5: found 587 genes
[ 2018-08-03 16:36:01 ] INFO Contrast group3_vs_group7: found 465 genes
[ 2018-08-03 16:36:01 ] INFO Contrast group3_vs_group13: found 557 genes
[ 2018-08-03 16:36:01 ] INFO Contrast group5_vs_group7: found 923 genes
[ 2018-08-03 16:36:01 ] INFO Contrast group5_vs_group13: found 363 genes
[ 2018-08-03 16:36:01 ] INFO Contrast group6_vs_group8: found 747 genes
[ 2018-08-03 16:36:01 ] INFO Contrast group7_vs_group13: found 824 genes
[ 2018-08-03 16:36:01 ] INFO Contrast group15_vs_group16: found 25 genes
[ 2018-08-03 16:36:01 ] INFO Contrast group13_vs_group15: found 180 genes
[ 2018-08-03 16:36:01 ] INFO Running statistical tests with: edger
[ 2018-08-03 16:36:19 ] INFO Contrast: group1_vs_group3
[ 2018-08-03 16:36:21 ] INFO Contrast: group2_vs_group4
[ 2018-08-03 16:36:23 ] INFO Contrast: group3_vs_group5
[ 2018-08-03 16:36:25 ] INFO Contrast: group3_vs_group7
[ 2018-08-03 16:36:27 ] INFO Contrast: group3_vs_group13
[ 2018-08-03 16:36:29 ] INFO Contrast: group5_vs_group7
[ 2018-08-03 16:36:31 ] INFO Contrast: group5_vs_group13
[ 2018-08-03 16:36:33 ] INFO Contrast: group6_vs_group8
[ 2018-08-03 16:36:35 ] INFO Contrast: group7_vs_group13
[ 2018-08-03 16:36:36 ] INFO Contrast: group15_vs_group16
[ 2018-08-03 16:36:38 ] INFO Contrast: group13_vs_group15
[ 2018-08-03 16:36:39 ] INFO Contrast group1_vs_group3: found 247 genes
[ 2018-08-03 16:36:39 ] INFO Contrast group2_vs_group4: found 867 genes
[ 2018-08-03 16:36:39 ] INFO Contrast group3_vs_group5: found 1205 genes
[ 2018-08-03 16:36:39 ] INFO Contrast group3_vs_group7: found 935 genes
[ 2018-08-03 16:36:39 ] INFO Contrast group3_vs_group13: found 860 genes
[ 2018-08-03 16:36:39 ] INFO Contrast group5_vs_group7: found 1180 genes
[ 2018-08-03 16:36:39 ] INFO Contrast group5_vs_group13: found 423 genes
[ 2018-08-03 16:36:39 ] INFO Contrast group6_vs_group8: found 1170 genes
[ 2018-08-03 16:36:39 ] INFO Contrast group7_vs_group13: found 1099 genes
[ 2018-08-03 16:36:39 ] INFO Contrast group15_vs_group16: found 142 genes
[ 2018-08-03 16:36:39 ] INFO Contrast group13_vs_group15: found 538 genes
[ 2018-08-03 16:36:39 ] INFO Running statistical tests with: limma
[ 2018-08-03 16:36:40 ] INFO Contrast: group1_vs_group3
[ 2018-08-03 16:36:42 ] INFO Contrast: group2_vs_group4
[ 2018-08-03 16:36:45 ] INFO Contrast: group3_vs_group5
[ 2018-08-03 16:36:48 ] INFO Contrast: group3_vs_group7
[ 2018-08-03 16:36:50 ] INFO Contrast: group3_vs_group13
[ 2018-08-03 16:36:53 ] INFO Contrast: group5_vs_group7
[ 2018-08-03 16:36:55 ] INFO Contrast: group5_vs_group13
[ 2018-08-03 16:36:57 ] INFO Contrast: group6_vs_group8
[ 2018-08-03 16:37:00 ] INFO Contrast: group7_vs_group13
[ 2018-08-03 16:37:02 ] INFO Contrast: group15_vs_group16
[ 2018-08-03 16:37:05 ] INFO Contrast: group13_vs_group15
[ 2018-08-03 16:37:07 ] INFO Contrast group1_vs_group3: found 303 genes
[ 2018-08-03 16:37:07 ] INFO Contrast group2_vs_group4: found 1795 genes
[ 2018-08-03 16:37:07 ] INFO Contrast group3_vs_group5: found 1819 genes
[ 2018-08-03 16:37:07 ] INFO Contrast group3_vs_group7: found 952 genes
[ 2018-08-03 16:37:07 ] INFO Contrast group3_vs_group13: found 1101 genes
[ 2018-08-03 16:37:07 ] INFO Contrast group5_vs_group7: found 1599 genes
[ 2018-08-03 16:37:07 ] INFO Contrast group5_vs_group13: found 1431 genes
[ 2018-08-03 16:37:07 ] INFO Contrast group6_vs_group8: found 1941 genes
[ 2018-08-03 16:37:07 ] INFO Contrast group7_vs_group13: found 1541 genes
[ 2018-08-03 16:37:07 ] INFO Contrast group15_vs_group16: found 1367 genes
[ 2018-08-03 16:37:07 ] INFO Contrast group13_vs_group15: found 1514 genes
[ 2018-08-03 16:37:07 ] INFO Running statistical tests with: nbpseq
[ 2018-08-03 16:37:07 ] INFO Contrast: group1_vs_group3
[ 2018-08-03 16:37:29 ] INFO Contrast: group2_vs_group4
[ 2018-08-03 16:37:52 ] INFO Contrast: group3_vs_group5
[ 2018-08-03 16:38:13 ] INFO Contrast: group3_vs_group7
[ 2018-08-03 16:38:33 ] INFO Contrast: group3_vs_group13
[ 2018-08-03 16:38:52 ] INFO Contrast: group5_vs_group7
[ 2018-08-03 16:39:13 ] INFO Contrast: group5_vs_group13
[ 2018-08-03 16:39:34 ] INFO Contrast: group6_vs_group8
[ 2018-08-03 16:39:57 ] INFO Contrast: group7_vs_group13
[ 2018-08-03 16:40:16 ] INFO Contrast: group15_vs_group16
[ 2018-08-03 16:40:33 ] INFO Contrast: group13_vs_group15
[ 2018-08-03 16:40:51 ] INFO Contrast group1_vs_group3: found 437 genes
[ 2018-08-03 16:40:51 ] INFO Contrast group2_vs_group4: found 1382 genes
[ 2018-08-03 16:40:51 ] INFO Contrast group3_vs_group5: found 1286 genes
[ 2018-08-03 16:40:51 ] INFO Contrast group3_vs_group7: found 1380 genes
[ 2018-08-03 16:40:51 ] INFO Contrast group3_vs_group13: found 1176 genes
[ 2018-08-03 16:40:51 ] INFO Contrast group5_vs_group7: found 1727 genes
[ 2018-08-03 16:40:51 ] INFO Contrast group5_vs_group13: found 746 genes
[ 2018-08-03 16:40:51 ] INFO Contrast group6_vs_group8: found 1277 genes
[ 2018-08-03 16:40:51 ] INFO Contrast group7_vs_group13: found 1681 genes
[ 2018-08-03 16:40:51 ] INFO Contrast group15_vs_group16: found 127 genes
[ 2018-08-03 16:40:51 ] INFO Contrast group13_vs_group15: found 560 genes
[ 2018-08-03 16:40:51 ] INFO Running statistical tests with: noiseq
[ 2018-08-03 16:40:51 ] INFO Contrast: group1_vs_group3
[ 2018-08-03 16:41:26 ] INFO Contrast: group2_vs_group4
[ 2018-08-03 16:42:07 ] INFO Contrast: group3_vs_group5
[ 2018-08-03 16:42:42 ] INFO Contrast: group3_vs_group7
[ 2018-08-03 16:43:17 ] INFO Contrast: group3_vs_group13
[ 2018-08-03 16:43:49 ] INFO Contrast: group5_vs_group7
[ 2018-08-03 16:44:24 ] INFO Contrast: group5_vs_group13
[ 2018-08-03 16:44:58 ] INFO Contrast: group6_vs_group8
[ 2018-08-03 16:45:40 ] INFO Contrast: group7_vs_group13
[ 2018-08-03 16:46:12 ] INFO Contrast: group15_vs_group16
[ 2018-08-03 16:46:49 ] INFO Contrast: group13_vs_group15
[ 2018-08-03 16:47:27 ] INFO Contrast group1_vs_group3: found 4 genes
[ 2018-08-03 16:47:27 ] INFO Contrast group2_vs_group4: found 1112 genes
[ 2018-08-03 16:47:27 ] INFO Contrast group3_vs_group5: found 642 genes
[ 2018-08-03 16:47:27 ] INFO Contrast group3_vs_group7: found 2023 genes
[ 2018-08-03 16:47:27 ] INFO Contrast group3_vs_group13: found 543 genes
[ 2018-08-03 16:47:27 ] INFO Contrast group5_vs_group7: found 1539 genes
[ 2018-08-03 16:47:27 ] INFO Contrast group5_vs_group13: found 611 genes
[ 2018-08-03 16:47:27 ] INFO Contrast group6_vs_group8: found 650 genes
[ 2018-08-03 16:47:27 ] INFO Contrast group7_vs_group13: found 9910 genes
[ 2018-08-03 16:47:27 ] INFO Contrast group15_vs_group16: found 60 genes
[ 2018-08-03 16:47:27 ] INFO Contrast group13_vs_group15: found 420 genes
[ 2018-08-03 16:47:27 ] INFO Performing meta-analysis with pandora
[ 2018-08-03 16:47:28 ] INFO Building output files...
[ 2018-08-03 16:47:29 ] INFO Contrast: group1_vs_group3
[ 2018-08-03 16:47:29 ] INFO Adding non-filtered data...
[ 2018-08-03 16:47:29 ] INFO binding annotation...
[ 2018-08-03 16:47:30 ] INFO binding p-values...
[ 2018-08-03 16:47:31 ] INFO binding FDRs...
[ 2018-08-03 16:47:31 ] INFO binding meta p-values...
[ 2018-08-03 16:47:32 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:47:32 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:47:32 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:47:32 ] INFO binding normalized mean counts...
[ 2018-08-03 16:47:33 ] INFO binding normalized mean counts...
[ 2018-08-03 16:47:34 ] INFO binding all normalized counts for group1...
[ 2018-08-03 16:47:36 ] INFO binding all normalized counts for group3...
[ 2018-08-03 16:47:37 ] INFO binding filtering flags...
[ 2018-08-03 16:47:38 ] INFO Writing output...
[ 2018-08-03 16:47:38 ] INFO Adding filtered data...
[ 2018-08-03 16:47:38 ] INFO binding annotation...
[ 2018-08-03 16:47:38 ] INFO binding p-values...
[ 2018-08-03 16:47:38 ] INFO binding FDRs...
[ 2018-08-03 16:47:38 ] INFO binding meta p-values...
[ 2018-08-03 16:47:38 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:47:38 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:47:38 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:47:38 ] INFO binding normalized mean counts...
[ 2018-08-03 16:47:39 ] INFO binding normalized mean counts...
[ 2018-08-03 16:47:40 ] INFO binding all normalized counts for group1...
[ 2018-08-03 16:47:40 ] INFO binding all normalized counts for group3...
[ 2018-08-03 16:47:40 ] INFO binding filtering flags...
[ 2018-08-03 16:47:41 ] INFO Writing output...
[ 2018-08-03 16:47:44 ] INFO Contrast: group2_vs_group4
[ 2018-08-03 16:47:44 ] INFO Adding non-filtered data...
[ 2018-08-03 16:47:44 ] INFO binding annotation...
[ 2018-08-03 16:47:45 ] INFO binding p-values...
[ 2018-08-03 16:47:45 ] INFO binding FDRs...
[ 2018-08-03 16:47:46 ] INFO binding meta p-values...
[ 2018-08-03 16:47:46 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:47:47 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:47:47 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:47:47 ] INFO binding normalized mean counts...
[ 2018-08-03 16:47:48 ] INFO binding normalized mean counts...
[ 2018-08-03 16:47:49 ] INFO binding all normalized counts for group2...
[ 2018-08-03 16:47:50 ] INFO binding all normalized counts for group4...
[ 2018-08-03 16:47:51 ] INFO binding filtering flags...
[ 2018-08-03 16:47:52 ] INFO Writing output...
[ 2018-08-03 16:47:53 ] INFO Adding filtered data...
[ 2018-08-03 16:47:53 ] INFO binding annotation...
[ 2018-08-03 16:47:53 ] INFO binding p-values...
[ 2018-08-03 16:47:53 ] INFO binding FDRs...
[ 2018-08-03 16:47:53 ] INFO binding meta p-values...
[ 2018-08-03 16:47:53 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:47:53 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:47:53 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:47:53 ] INFO binding normalized mean counts...
[ 2018-08-03 16:47:54 ] INFO binding normalized mean counts...
[ 2018-08-03 16:47:55 ] INFO binding all normalized counts for group2...
[ 2018-08-03 16:47:55 ] INFO binding all normalized counts for group4...
[ 2018-08-03 16:47:55 ] INFO binding filtering flags...
[ 2018-08-03 16:47:55 ] INFO Writing output...
[ 2018-08-03 16:47:59 ] INFO Contrast: group3_vs_group5
[ 2018-08-03 16:47:59 ] INFO Adding non-filtered data...
[ 2018-08-03 16:47:59 ] INFO binding annotation...
[ 2018-08-03 16:48:00 ] INFO binding p-values...
[ 2018-08-03 16:48:00 ] INFO binding FDRs...
[ 2018-08-03 16:48:01 ] INFO binding meta p-values...
[ 2018-08-03 16:48:01 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:48:01 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:48:02 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:48:02 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:03 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:04 ] INFO binding all normalized counts for group3...
[ 2018-08-03 16:48:06 ] INFO binding all normalized counts for group5...
[ 2018-08-03 16:48:07 ] INFO binding filtering flags...
[ 2018-08-03 16:48:08 ] INFO Writing output...
[ 2018-08-03 16:48:08 ] INFO Adding filtered data...
[ 2018-08-03 16:48:08 ] INFO binding annotation...
[ 2018-08-03 16:48:08 ] INFO binding p-values...
[ 2018-08-03 16:48:08 ] INFO binding FDRs...
[ 2018-08-03 16:48:08 ] INFO binding meta p-values...
[ 2018-08-03 16:48:08 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:48:09 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:48:09 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:48:09 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:10 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:10 ] INFO binding all normalized counts for group3...
[ 2018-08-03 16:48:10 ] INFO binding all normalized counts for group5...
[ 2018-08-03 16:48:10 ] INFO binding filtering flags...
[ 2018-08-03 16:48:11 ] INFO Writing output...
[ 2018-08-03 16:48:14 ] INFO Contrast: group3_vs_group7
[ 2018-08-03 16:48:14 ] INFO Adding non-filtered data...
[ 2018-08-03 16:48:14 ] INFO binding annotation...
[ 2018-08-03 16:48:15 ] INFO binding p-values...
[ 2018-08-03 16:48:16 ] INFO binding FDRs...
[ 2018-08-03 16:48:16 ] INFO binding meta p-values...
[ 2018-08-03 16:48:17 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:48:17 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:48:17 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:48:17 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:18 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:19 ] INFO binding all normalized counts for group3...
[ 2018-08-03 16:48:20 ] INFO binding all normalized counts for group7...
[ 2018-08-03 16:48:21 ] INFO binding filtering flags...
[ 2018-08-03 16:48:22 ] INFO Writing output...
[ 2018-08-03 16:48:22 ] INFO Adding filtered data...
[ 2018-08-03 16:48:22 ] INFO binding annotation...
[ 2018-08-03 16:48:22 ] INFO binding p-values...
[ 2018-08-03 16:48:22 ] INFO binding FDRs...
[ 2018-08-03 16:48:22 ] INFO binding meta p-values...
[ 2018-08-03 16:48:22 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:48:23 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:48:23 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:48:23 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:24 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:24 ] INFO binding all normalized counts for group3...
[ 2018-08-03 16:48:24 ] INFO binding all normalized counts for group7...
[ 2018-08-03 16:48:24 ] INFO binding filtering flags...
[ 2018-08-03 16:48:25 ] INFO Writing output...
[ 2018-08-03 16:48:28 ] INFO Contrast: group3_vs_group13
[ 2018-08-03 16:48:28 ] INFO Adding non-filtered data...
[ 2018-08-03 16:48:28 ] INFO binding annotation...
[ 2018-08-03 16:48:29 ] INFO binding p-values...
[ 2018-08-03 16:48:30 ] INFO binding FDRs...
[ 2018-08-03 16:48:30 ] INFO binding meta p-values...
[ 2018-08-03 16:48:31 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:48:31 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:48:31 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:48:31 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:32 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:33 ] INFO binding all normalized counts for group3...
[ 2018-08-03 16:48:34 ] INFO binding all normalized counts for group13...
[ 2018-08-03 16:48:35 ] INFO binding filtering flags...
[ 2018-08-03 16:48:36 ] INFO Writing output...
[ 2018-08-03 16:48:36 ] INFO Adding filtered data...
[ 2018-08-03 16:48:36 ] INFO binding annotation...
[ 2018-08-03 16:48:36 ] INFO binding p-values...
[ 2018-08-03 16:48:36 ] INFO binding FDRs...
[ 2018-08-03 16:48:36 ] INFO binding meta p-values...
[ 2018-08-03 16:48:36 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:48:37 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:48:37 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:48:37 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:37 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:39 ] INFO binding all normalized counts for group3...
[ 2018-08-03 16:48:39 ] INFO binding all normalized counts for group13...
[ 2018-08-03 16:48:39 ] INFO binding filtering flags...
[ 2018-08-03 16:48:40 ] INFO Writing output...
[ 2018-08-03 16:48:43 ] INFO Contrast: group5_vs_group7
[ 2018-08-03 16:48:43 ] INFO Adding non-filtered data...
[ 2018-08-03 16:48:43 ] INFO binding annotation...
[ 2018-08-03 16:48:44 ] INFO binding p-values...
[ 2018-08-03 16:48:44 ] INFO binding FDRs...
[ 2018-08-03 16:48:45 ] INFO binding meta p-values...
[ 2018-08-03 16:48:45 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:48:45 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:48:46 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:48:46 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:47 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:47 ] INFO binding all normalized counts for group5...
[ 2018-08-03 16:48:49 ] INFO binding all normalized counts for group7...
[ 2018-08-03 16:48:50 ] INFO binding filtering flags...
[ 2018-08-03 16:48:51 ] INFO Writing output...
[ 2018-08-03 16:48:51 ] INFO Adding filtered data...
[ 2018-08-03 16:48:51 ] INFO binding annotation...
[ 2018-08-03 16:48:51 ] INFO binding p-values...
[ 2018-08-03 16:48:51 ] INFO binding FDRs...
[ 2018-08-03 16:48:51 ] INFO binding meta p-values...
[ 2018-08-03 16:48:51 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:48:51 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:48:51 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:48:51 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:52 ] INFO binding normalized mean counts...
[ 2018-08-03 16:48:53 ] INFO binding all normalized counts for group5...
[ 2018-08-03 16:48:53 ] INFO binding all normalized counts for group7...
[ 2018-08-03 16:48:53 ] INFO binding filtering flags...
[ 2018-08-03 16:48:54 ] INFO Writing output...
[ 2018-08-03 16:48:57 ] INFO Contrast: group5_vs_group13
[ 2018-08-03 16:48:57 ] INFO Adding non-filtered data...
[ 2018-08-03 16:48:57 ] INFO binding annotation...
[ 2018-08-03 16:48:59 ] INFO binding p-values...
[ 2018-08-03 16:48:59 ] INFO binding FDRs...
[ 2018-08-03 16:49:00 ] INFO binding meta p-values...
[ 2018-08-03 16:49:00 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:49:00 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:49:01 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:49:01 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:02 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:03 ] INFO binding all normalized counts for group5...
[ 2018-08-03 16:49:04 ] INFO binding all normalized counts for group13...
[ 2018-08-03 16:49:05 ] INFO binding filtering flags...
[ 2018-08-03 16:49:06 ] INFO Writing output...
[ 2018-08-03 16:49:06 ] INFO Adding filtered data...
[ 2018-08-03 16:49:06 ] INFO binding annotation...
[ 2018-08-03 16:49:06 ] INFO binding p-values...
[ 2018-08-03 16:49:06 ] INFO binding FDRs...
[ 2018-08-03 16:49:06 ] INFO binding meta p-values...
[ 2018-08-03 16:49:06 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:49:06 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:49:06 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:49:06 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:07 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:08 ] INFO binding all normalized counts for group5...
[ 2018-08-03 16:49:08 ] INFO binding all normalized counts for group13...
[ 2018-08-03 16:49:08 ] INFO binding filtering flags...
[ 2018-08-03 16:49:08 ] INFO Writing output...
[ 2018-08-03 16:49:11 ] INFO Contrast: group6_vs_group8
[ 2018-08-03 16:49:11 ] INFO Adding non-filtered data...
[ 2018-08-03 16:49:11 ] INFO binding annotation...
[ 2018-08-03 16:49:12 ] INFO binding p-values...
[ 2018-08-03 16:49:13 ] INFO binding FDRs...
[ 2018-08-03 16:49:13 ] INFO binding meta p-values...
[ 2018-08-03 16:49:14 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:49:14 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:49:14 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:49:14 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:15 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:16 ] INFO binding all normalized counts for group6...
[ 2018-08-03 16:49:18 ] INFO binding all normalized counts for group8...
[ 2018-08-03 16:49:19 ] INFO binding filtering flags...
[ 2018-08-03 16:49:20 ] INFO Writing output...
[ 2018-08-03 16:49:20 ] INFO Adding filtered data...
[ 2018-08-03 16:49:20 ] INFO binding annotation...
[ 2018-08-03 16:49:20 ] INFO binding p-values...
[ 2018-08-03 16:49:20 ] INFO binding FDRs...
[ 2018-08-03 16:49:20 ] INFO binding meta p-values...
[ 2018-08-03 16:49:20 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:49:20 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:49:20 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:49:20 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:21 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:22 ] INFO binding all normalized counts for group6...
[ 2018-08-03 16:49:22 ] INFO binding all normalized counts for group8...
[ 2018-08-03 16:49:22 ] INFO binding filtering flags...
[ 2018-08-03 16:49:23 ] INFO Writing output...
[ 2018-08-03 16:49:26 ] INFO Contrast: group7_vs_group13
[ 2018-08-03 16:49:26 ] INFO Adding non-filtered data...
[ 2018-08-03 16:49:26 ] INFO binding annotation...
[ 2018-08-03 16:49:27 ] INFO binding p-values...
[ 2018-08-03 16:49:28 ] INFO binding FDRs...
[ 2018-08-03 16:49:28 ] INFO binding meta p-values...
[ 2018-08-03 16:49:28 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:49:29 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:49:29 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:49:29 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:30 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:31 ] INFO binding all normalized counts for group7...
[ 2018-08-03 16:49:32 ] INFO binding all normalized counts for group13...
[ 2018-08-03 16:49:33 ] INFO binding filtering flags...
[ 2018-08-03 16:49:34 ] INFO Writing output...
[ 2018-08-03 16:49:34 ] INFO Adding filtered data...
[ 2018-08-03 16:49:34 ] INFO binding annotation...
[ 2018-08-03 16:49:34 ] INFO binding p-values...
[ 2018-08-03 16:49:34 ] INFO binding FDRs...
[ 2018-08-03 16:49:34 ] INFO binding meta p-values...
[ 2018-08-03 16:49:34 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:49:35 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:49:35 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:49:35 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:36 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:37 ] INFO binding all normalized counts for group7...
[ 2018-08-03 16:49:37 ] INFO binding all normalized counts for group13...
[ 2018-08-03 16:49:37 ] INFO binding filtering flags...
[ 2018-08-03 16:49:38 ] INFO Writing output...
[ 2018-08-03 16:49:41 ] INFO Contrast: group15_vs_group16
[ 2018-08-03 16:49:41 ] INFO Adding non-filtered data...
[ 2018-08-03 16:49:41 ] INFO binding annotation...
[ 2018-08-03 16:49:42 ] INFO binding p-values...
[ 2018-08-03 16:49:42 ] INFO binding FDRs...
[ 2018-08-03 16:49:43 ] INFO binding meta p-values...
[ 2018-08-03 16:49:43 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:49:44 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:49:44 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:49:45 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:45 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:46 ] INFO binding all normalized counts for group15...
[ 2018-08-03 16:49:47 ] INFO binding all normalized counts for group16...
[ 2018-08-03 16:49:48 ] INFO binding filtering flags...
[ 2018-08-03 16:49:48 ] INFO Writing output...
[ 2018-08-03 16:49:49 ] INFO Adding filtered data...
[ 2018-08-03 16:49:49 ] INFO binding annotation...
[ 2018-08-03 16:49:49 ] INFO binding p-values...
[ 2018-08-03 16:49:49 ] INFO binding FDRs...
[ 2018-08-03 16:49:49 ] INFO binding meta p-values...
[ 2018-08-03 16:49:49 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:49:49 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:49:49 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:49:49 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:50 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:50 ] INFO binding all normalized counts for group15...
[ 2018-08-03 16:49:50 ] INFO binding all normalized counts for group16...
[ 2018-08-03 16:49:50 ] INFO binding filtering flags...
[ 2018-08-03 16:49:51 ] INFO Writing output...
[ 2018-08-03 16:49:54 ] INFO Contrast: group13_vs_group15
[ 2018-08-03 16:49:54 ] INFO Adding non-filtered data...
[ 2018-08-03 16:49:54 ] INFO binding annotation...
[ 2018-08-03 16:49:55 ] INFO binding p-values...
[ 2018-08-03 16:49:55 ] INFO binding FDRs...
[ 2018-08-03 16:49:56 ] INFO binding meta p-values...
[ 2018-08-03 16:49:56 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:49:56 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:49:56 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:49:57 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:57 ] INFO binding normalized mean counts...
[ 2018-08-03 16:49:58 ] INFO binding all normalized counts for group13...
[ 2018-08-03 16:49:59 ] INFO binding all normalized counts for group15...
[ 2018-08-03 16:50:00 ] INFO binding filtering flags...
[ 2018-08-03 16:50:01 ] INFO Writing output...
[ 2018-08-03 16:50:01 ] INFO Adding filtered data...
[ 2018-08-03 16:50:01 ] INFO binding annotation...
[ 2018-08-03 16:50:01 ] INFO binding p-values...
[ 2018-08-03 16:50:01 ] INFO binding FDRs...
[ 2018-08-03 16:50:01 ] INFO binding meta p-values...
[ 2018-08-03 16:50:01 ] INFO binding adjusted meta p-values...
[ 2018-08-03 16:50:01 ] INFO binding natural normalized fold changes...
[ 2018-08-03 16:50:01 ] INFO binding log2 normalized fold changes...
[ 2018-08-03 16:50:01 ] INFO binding normalized mean counts...
[ 2018-08-03 16:50:02 ] INFO binding normalized mean counts...
[ 2018-08-03 16:50:03 ] INFO binding all normalized counts for group13...
[ 2018-08-03 16:50:03 ] INFO binding all normalized counts for group15...
[ 2018-08-03 16:50:03 ] INFO binding filtering flags...
[ 2018-08-03 16:50:04 ] INFO Writing output...
[ 2018-08-03 16:50:06 ] INFO Creating quality control graphs...
[ 2018-08-03 16:50:06 ] INFO Plotting in png format...
[ 2018-08-03 16:50:06 ] INFO Plotting mds...
[ 2018-08-03 16:50:07 ] INFO Plotting biodetection...
[ 2018-08-03 16:50:13 ] INFO Plotting countsbio...
[ 2018-08-03 16:50:22 ] INFO Plotting saturation...
[ 2018-08-03 16:50:55 ] INFO Plotting readnoise...
[ 2018-08-03 16:51:18 ] INFO Plotting correl...
[ 2018-08-03 16:51:19 ] INFO Plotting boxplot...
[ 2018-08-03 16:51:20 ] INFO Plotting gcbias...
[ 2018-08-03 16:51:26 ] INFO Plotting lengthbias...
[ 2018-08-03 16:51:30 ] INFO Plotting meandiff...
[ 2018-08-03 16:51:37 ] INFO Plotting meanvar...
[ 2018-08-03 16:52:56 ] INFO Plotting boxplot...
[ 2018-08-03 16:52:57 ] INFO Plotting gcbias...
[ 2018-08-03 16:53:03 ] INFO Plotting lengthbias...
[ 2018-08-03 16:53:07 ] INFO Plotting meandiff...
[ 2018-08-03 16:53:14 ] INFO Plotting meanvar...
[ 2018-08-03 16:54:35 ] INFO Plotting biodist...
[ 2018-08-03 16:54:35 ] INFO Contrast: group1_vs_group3
[ 2018-08-03 16:54:36 ] INFO Contrast: group2_vs_group4
[ 2018-08-03 16:54:36 ] INFO Contrast: group3_vs_group5
[ 2018-08-03 16:54:37 ] INFO Contrast: group3_vs_group7
[ 2018-08-03 16:54:37 ] INFO Contrast: group3_vs_group13
[ 2018-08-03 16:54:37 ] INFO Contrast: group5_vs_group7
[ 2018-08-03 16:54:38 ] INFO Contrast: group5_vs_group13
[ 2018-08-03 16:54:38 ] INFO Contrast: group6_vs_group8
[ 2018-08-03 16:54:38 ] INFO Contrast: group7_vs_group13
[ 2018-08-03 16:54:39 ] INFO Contrast: group15_vs_group16
[ 2018-08-03 16:54:39 ] INFO Contrast: group13_vs_group15
[ 2018-08-03 16:54:39 ] INFO Plotting volcano...
[ 2018-08-03 16:54:39 ] INFO Contrast: group1_vs_group3
[ 2018-08-03 16:54:40 ] INFO Contrast: group2_vs_group4
[ 2018-08-03 16:54:41 ] INFO Contrast: group3_vs_group5
[ 2018-08-03 16:54:42 ] INFO Contrast: group3_vs_group7
[ 2018-08-03 16:54:42 ] INFO Contrast: group3_vs_group13
[ 2018-08-03 16:54:43 ] INFO Contrast: group5_vs_group7
[ 2018-08-03 16:54:44 ] INFO Contrast: group5_vs_group13
[ 2018-08-03 16:54:45 ] INFO Contrast: group6_vs_group8
[ 2018-08-03 16:54:45 ] INFO Contrast: group7_vs_group13
[ 2018-08-03 16:54:46 ] INFO Contrast: group15_vs_group16
[ 2018-08-03 16:54:47 ] INFO Contrast: group13_vs_group15
[ 2018-08-03 16:54:48 ] INFO Plotting deheatmap...
[ 2018-08-03 16:54:48 ] INFO Contrast: group1_vs_group3
[ 2018-08-03 16:55:50 ] INFO Contrast: group2_vs_group4
[ 2018-08-03 16:56:51 ] INFO Contrast: group3_vs_group5
[ 2018-08-03 16:57:50 ] INFO Contrast: group3_vs_group7
[ 2018-08-03 16:58:48 ] INFO Contrast: group3_vs_group13
[ 2018-08-03 16:59:45 ] INFO Contrast: group5_vs_group7
[ 2018-08-03 17:00:45 ] INFO Contrast: group5_vs_group13
[ 2018-08-03 17:01:43 ] INFO Contrast: group6_vs_group8
[ 2018-08-03 17:02:43 ] INFO Contrast: group7_vs_group13
[ 2018-08-03 17:03:40 ] INFO Contrast: group15_vs_group16
[ 2018-08-03 17:04:37 ] INFO Contrast: group13_vs_group15
[ 2018-08-03 17:05:36 ] INFO Plotting filtered...
[ 2018-08-03 17:05:36 ] INFO Plotting in pdf format...
[ 2018-08-03 17:05:36 ] INFO Plotting mds...
[ 2018-08-03 17:05:37 ] INFO Plotting biodetection...
[ 2018-08-03 17:05:40 ] INFO Plotting countsbio...
[ 2018-08-03 17:05:44 ] INFO Plotting saturation...
[ 2018-08-03 17:06:13 ] INFO Plotting readnoise...
[ 2018-08-03 17:06:37 ] INFO Plotting correl...
[ 2018-08-03 17:06:38 ] INFO Plotting boxplot...
[ 2018-08-03 17:06:39 ] INFO Plotting gcbias...
[ 2018-08-03 17:06:46 ] INFO Plotting lengthbias...
[ 2018-08-03 17:06:51 ] INFO Plotting meandiff...
[ 2018-08-03 17:07:01 ] INFO Plotting meanvar...
[ 2018-08-03 17:08:20 ] INFO Plotting boxplot...
[ 2018-08-03 17:08:21 ] INFO Plotting gcbias...
[ 2018-08-03 17:08:28 ] INFO Plotting lengthbias...
[ 2018-08-03 17:08:33 ] INFO Plotting meandiff...
[ 2018-08-03 17:08:43 ] INFO Plotting meanvar...
[ 2018-08-03 17:10:07 ] INFO Plotting biodist...
[ 2018-08-03 17:10:07 ] INFO Contrast: group1_vs_group3
[ 2018-08-03 17:10:07 ] INFO Contrast: group2_vs_group4
[ 2018-08-03 17:10:07 ] INFO Contrast: group3_vs_group5
[ 2018-08-03 17:10:07 ] INFO Contrast: group3_vs_group7
[ 2018-08-03 17:10:08 ] INFO Contrast: group3_vs_group13
[ 2018-08-03 17:10:08 ] INFO Contrast: group5_vs_group7
[ 2018-08-03 17:10:08 ] INFO Contrast: group5_vs_group13
[ 2018-08-03 17:10:08 ] INFO Contrast: group6_vs_group8
[ 2018-08-03 17:10:09 ] INFO Contrast: group7_vs_group13
[ 2018-08-03 17:10:09 ] INFO Contrast: group15_vs_group16
[ 2018-08-03 17:10:09 ] INFO Contrast: group13_vs_group15
[ 2018-08-03 17:10:09 ] INFO Plotting volcano...
[ 2018-08-03 17:10:09 ] INFO Contrast: group1_vs_group3
[ 2018-08-03 17:10:10 ] INFO Contrast: group2_vs_group4
[ 2018-08-03 17:10:10 ] INFO Contrast: group3_vs_group5
[ 2018-08-03 17:10:10 ] INFO Contrast: group3_vs_group7
[ 2018-08-03 17:10:11 ] INFO Contrast: group3_vs_group13
[ 2018-08-03 17:10:11 ] INFO Contrast: group5_vs_group7
[ 2018-08-03 17:10:12 ] INFO Contrast: group5_vs_group13
[ 2018-08-03 17:10:12 ] INFO Contrast: group6_vs_group8
[ 2018-08-03 17:10:12 ] INFO Contrast: group7_vs_group13
[ 2018-08-03 17:10:13 ] INFO Contrast: group15_vs_group16
[ 2018-08-03 17:10:13 ] INFO Contrast: group13_vs_group15
[ 2018-08-03 17:10:14 ] INFO Plotting deheatmap...
[ 2018-08-03 17:10:14 ] INFO Contrast: group1_vs_group3
[ 2018-08-03 17:11:15 ] INFO Contrast: group2_vs_group4
[ 2018-08-03 17:12:15 ] INFO Contrast: group3_vs_group5
[ 2018-08-03 17:13:14 ] INFO Contrast: group3_vs_group7
[ 2018-08-03 17:14:12 ] INFO Contrast: group3_vs_group13
[ 2018-08-03 17:15:09 ] INFO Contrast: group5_vs_group7
[ 2018-08-03 17:16:09 ] INFO Contrast: group5_vs_group13
[ 2018-08-03 17:17:07 ] INFO Contrast: group6_vs_group8
[ 2018-08-03 17:18:08 ] INFO Contrast: group7_vs_group13
[ 2018-08-03 17:19:04 ] INFO Contrast: group15_vs_group16
[ 2018-08-03 17:20:01 ] INFO Contrast: group13_vs_group15
[ 2018-08-03 17:20:59 ] INFO Plotting filtered...
[ 2018-08-03 17:20:59 ] INFO Creating HTML report...
[ 2018-08-03 17:20:59 ] INFO Compressing figures...

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