In a given RNA-Seq differential gene expression analysis, one might perform a gene ontology analysis by setting cutoffs to create a gene set (e.g. abs(Log2FC) > 1, p < 0.05). Here, it is possible to use raw p-values (includes more true positive and false-positive DEGs), or FDR-correct p-values (includes less true positives but a smaller-fraction of false positives). Of course, the GO analysis needs to be corrected with FDR as well.
My question is, what are your thoughts for creating gene sets using p-values or q-values? In my mind, any set of filters that are selected A priori should be fine to create a gene set to test for enrichment, and as long as the GO-enrichment tests are corrected using FDR or a similar method, the results are still statistically robust.