FDR results from simulation study. Boxplots of observed FDR of tests for differential expression for simulations runs both with and without variance filtering. Plots (A) and (B) are boxplots for simulation scenarios with a "clumpy dependence" among genes using the Benjamini-Hochberg (BH) and q-value methods, respectively. Plots (C) and (D) are boxplots for simulation scenarios modeling independence among genes using the BH and q-value methods, respectively. The nominal FDR level = 0.05 is represented by the horizontal dashed lines on plots.