Figure 2

Detection rates in simulated data sets as a function of increasing inter-class separation. For each gene set analysis method, the data were permuted 2,000 times to generate p-values for each gene set, within each simulation. FDR-adjusted p-values of less than 0.05 were used to indicate significance. (a) Gene sets active in one class and inactive in the other, On-Off (D), with pairwise correlations of 0.1. (b) Gene sets were active in both classes, On-On (D), with pairwise correlations of 0.1. (c) Gene sets active in one class and inactive in the other, On-Off (D), with pairwise correlations of 0.25. (d) Gene sets were active in both classes, On-On (D), with pairwise correlations of 0.25.