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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