Table 2.

Results of Simulation Experiment. Gene sets = relevant gene sets used in the computation of evaluation measures (test size, area under ROC curve, power or stability); Ho Tested = the null hypothesis being tested; MMevct = mixed model with eigenvectors as random effects to account for the covariance structure between genes; MMrstudent = mixed model with studentized residuals as random effects; globalANCOVA = the globalANCOVA method (Hummel et al. 2008); Fisher05 = Fisher’s exact test with nominal p-value 0.05 as threshold for selecting significant genes. See text for details of the simulation experiment.

Gene Sets	Ho Tested	MMevct	MMrstudent	globalANCOVA	Fisher05
Test Size
175–522	central	0.049	0.106	0.351	0.06
349–522	global	0.052	0.109	0.04	0.034
Power
1–174	central	0.73	0.736	0.833	0.299
1–348	global	0.388	0.42	0.747	0.193
Area Under ROC Curve
1–522	central	0.951	0.911	0.785	0.696
1–522	global	0.783	0.759	0.954	0.791
Stability (av. pair-wise spearman rank correlations)
1–522		0.902	0.964	0.881	0.702