Figure 7. Summary of performance of the packages edgeR, DESeq and their Polyfit extensions in estimating the FDR for genes out to a significance point corresponding to half the number of truly DE genes.

(See plots (B), (D) and (F) in Fig. 5 and analogous plots in Figs. S1–S20). Experiments were done with n = 2, 4, 6 and 10 simulated replicates of synthetic data in which 1, 5, 10 and 15% of genes are DE.