Figure 6.

Boxplots generated by null p-values yielded after permutation is applied to the simulated data, for varying proportions of features left in the data (x-axis) using the fold-change filter. For comparison, the distribution yielded without filtering is shown (leftmost boxplot). Lines represent the achieved FDR using each of the methods aimed at 5% control level: BH (dashed line with triangles), aBH (dashed-and-dotted line with crosses), BY (dotted line). For comparison, the Bonferroni correction is also shown (solid line). Above each boxplot the p-value yielded by our test for FDR bias is given ('***' for < 0.001). The solid thin straight line at 5% represents the FDR threshold used.