Table 1 Number of false differential expression genes predicted by each method at adjusted P values (or false discovery rate) ≤0.05 separated by gene read count quantiles.
From: Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
Expression quantile | Cuffdiff | DESeq | edgeR | limmaQN | limmaVoom | PoissonSeq | baySeq |
|---|---|---|---|---|---|---|---|
100% (high expression) | 28 | 5 | 3 | 0 | 0 | 7 | 1 |
75% | 76 | 6 | 0 | 0 | 0 | 0 | 0 |
50% | 84 | 27 | 1 | 2 | 0 | 0 | 0 |
25% (low expression) | 5 | 9 | 0 | 87 | 0 | 0 | 0 |
Total | 193 | 47 | 4 | 89 | 0 | 7 | 1 |