Figure 4

True false discovery rates. True false discovery rates (FDR) observed for an imposed FDR threshold of 0.05, for the nine methods returning adjusted p-values or FDR estimates, in simulation studies $B_0^{1250}$ (panel A), $B_{625}^{625}$ (panel B), $B_0^{4000}$ (panel C) $B_{2000}^{2000}$, (panel D), $S_{625}^{625}$ (panel E) and $R_{625}^{625}$ (panel F). With only two samples per condition, three of the methods (vst+limma, voom+limma and SAMseq) did not call any DE genes, and the FDR was considered to be undefined.