Fig. 2

Venn diagram for the detected DEGs reported by different methods in the real data-based simulation. Expression levels of 10000 genes were simulated, among them 30 % genes are up regulated, 30 % genes are down regulated and 40 % genes are non-DE genes. After removing genes with low counts, 6454 genes remain. The Venn diagrams (from left to right) show the intersection between true DEGs and top 10 %, 20 % and 30 % genes ranked by DEseq, eBayes and our method, respectively. At 10 % cutoff, the detected true positives are 994/3844 = 25.8 % (our), 980/3844 = 25.4 % (DEseq) and 988/3844 = 25.7 % (eBayes), respectively. At 20 % cutoff, the detected true positive are 1922/3844 = 50.0 % (our), 1858/3844 = 48.3 % (DEseq) and 1863/3844 = 48.5 % (eBayes), respectively. At 30 % cutoff, the detected true positive are 2626/3844 = 68.3 % (our), 2508/3844 = 65.4 % (DEseq) and 2519/3844 = 65.9 % (eBayes)