Calibration analysis. Plot of the average true fraction of false discoveries versus the average q-value over 100 simulation runs. The identity line indicates the ideal scenario of a perfect FDR-control rate; being above the identity line indicates anti-conservative behavior, and being below the identity line indicates conservative behavior. Simulations use the permutation null (top panel) or the passenger null (bottom panel). The gene-oriented method shows very anti-conservative behavior while the patient-oriented methods are generally calibrated or conservative.