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Table 1 Differential expression calls

From: Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls

EE DEC raw sva sva+FC sva+FC+AE
r-Make limma 7226 8078 4498 [56%] 3058 [38%]
  edgeR 7314 8720 4908 [56%] 3058 [35%]
  DESeq2 6974 8380 4552 [54%] 3060 [37%]
Subread limma 9772 9557 4795 [50%] 3016 [32%]
  edgeR 10202 10522 5398 [51%] 3036 [29%]
  DESeq2 9308 9709 4662 [48%] 3052 [31%]
TopHat2/ limma 8854 8782 4450 [51%] 3058 [35%]
Cufflinks2 edgeR 7329 7104 4386 [62%] 3018 [42%]
  DESeq2 8536 8489 4077 [48%] 3061 [36%]
SHRiMP2/ limma 8952 8276 4086 [49%] 3045 [37%]
BitSeq edgeR 8791 8663 4526 [52%] 3025 [35%]
  DESeq2 7590 7878 3804 [48%] 3038 [39%]
kallisto limma 8984 8851 4410 [50%] 3022 [34%]
  edgeR 9356 9284 4666 [50%] 3039 [33%]
  DESeq2 8016 8296 3915 [47%] 3044 [37%]
  1. The table displays the number of differential expression calls, reflecting sensitivity, as obtained after specific analysis steps. For all combinations of methods for expression estimation and differential expression calling, we compare the typical numbers of genes classified as differentially expressed (q<5%). The columns show median results across sites for: raw expression estimates; expression estimates after svaseq correction; expression estimates after svaseq correction and application of additional filters for effect strength, i.e., fold-change (|log2F C|>1); and expression estimates after svaseq correction and application of additional filters for effect strength (|log2F C|>1) and minimum average expression (AE thresholds in Table 2). The last two columns also give a percentage relative to the numbers of genes found after svaseq correction and no additional filters. This highlights that the additional filtering for weak expression removes only a further 16% of genes originally classified as differentially expressed in addition to the ones already removed by the usual filters for log-fold change, affecting just 2.5% of all genes