Fig. 4.

Result of a two-sample, unpaired t-test on simulated data using two simulation methods: Leek’s linear model (left panel) and Dwork’s experiment (right panel). Simulation parameters: 5000 attributes (500 functional) with 50 cases and 50 controls. Note the vertical scales are different. Each point represents the true positive rate (red) and false positive rate (blue) for a simulated data set with the effect size/bias given on the horizontal axis. The true and false percentages were computed based on an adjusted P-value of 0.05. The vertical dash line displays the effect bias used in Dwork’s simulation ($6/\sqrt{n}$). The vertical solid line displays the value of effect size we choose for the linear model simulation and its corresponding bias in Dwork’s simulation that yields the same detection power (∼ 12%) (Color version of this figure is available at Bioinformatics online.)