Figure 4.

Achieved FDR as function of the fraction filtered out x for the different filter statistics, fixing the FDR with each method at 0.05. Values shown are the mean FDR over 1000 simulated datasets (the variability of the FDR is small - not shown). Filters are: dashed line = variance, dotted = signal, dashed-and-dotted = fold change. In all cases the proportion of non-differentially expressed genes is fixed at 0.8. The q-value method cannot be computed for the fold-change filter as in this cases the p-value range changes.