False positive rates are greatly increased using independence assumption methods, GO Biological Process categories. The proportion of permutations in which at least one GO Biological Process category is called significant using an independence assumption method with a Bonferroni correction (α = 0.05), the Benjamini & Hochberg FDR (α = 0.05, 0.10), and the resampling approach described in this manuscript. Red lines = 5% & 10%.
Gatti et al. BMC Genomics 2010 11:574 doi:10.1186/1471-2164-11-574