of the two primary categories, we used Fisher’s method for combining P values with Brown’s correction, which is an extension of Fisher’s method that accounts for correlation between the different enrichment test statistics 116. Then, within category, P values were Bonferroni corrected across all gene sets tested, yielding two P values for each gene set. Lastly, these two P values arising from the two categories of tests (gene and subject sampling) were again Bonferroni-corrected to adjust for the twofold testing, and the minimum of the two was reported (Supplementary data file 4).
