Multiple hypothesis correction with multiple gene sets
I’ve multiple gene sets (N) that are not necessarily disjoint. Typically, performing GO enrichment using any off-the-shelf tool provides raw and adjusted p-values for each gene set. My understanding is that no further correction is typically applied and adjusted p-values per input gene set are reported.
However, this does not correct for the fact that we are testing N different gene sets. When displaying terms from all gene sets in a figure panel, the corrected values would be inflated in the context of the entire panel. Would it be more appropriate to instead correct raw p-values pooled across all input gene sets together? What’s the preferred approach?
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