Figure 2

Permutation and moment-based p-values are tightly correlated. Permutation p-values (x-axis) versus moment-based p-values (y-axis) for 6,303 gene sets. The left two column represents results for a linear test statistic versus the beta and Gaussian approximations; the right-most column represents results for the sum of squares statistic versus the χ ² approximation. Data come from three genome-wide expression studies. We applied the transformation − log10(p) to stretch the lower range of these distributions for a more informative visual. Red dotted lines represent the line y=x.