Fig. 7

False discovery rate increases when methods are challenged with very uneven library sizes. Real data from one body site was randomly divided into two groups, creating a situation in which there should be no true positives. a Uneven library sizes, 3 samples per group. b Uneven library sizes, 100 samples per group. For uneven library sizes, the group means differed by 10× (e.g., 40,000 sequences per sample vs. 4000 sequences per sample). The 45-degree line shows where the nominal FDR should equal the observed FDR. c Cumulative distribution functions of the effect sizes for 3, 20, and 100 samples per group presented in a and b. Voom was excluded because it was found to have a higher type I error rate than fitZIG