Figure 2.

Precision (1-FDR) of gene set queries methods with Pearson based p-values calibrated on GEO and CMAP compared to permutation based p-values and no permutation. Also included, for comparison are GSEA q-value (based on FDR) and GSEA p-value (based on FWER). We compared Precision across the various queries for threshold of gene sets (N) plotted on the x-axis (as described in Methods).