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ctlab / fgsea

Fast Gene Set Enrichment Analysis
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fgsea giving identical padj values across many pathways #144

Closed johnse closed 9 months ago

johnse commented 10 months ago

Hi, I'm trying to run fgsea as follows:

set.seed(9315) D_EV_GOBP <- fgseaMultilevel(pathways = pathways.GOBP, stats = D_EV_gsea_genelist, minSize = 5, maxSize = 500) %>% arrange(desc(NES)) however when I do this I'm getting different p-values but identical padj across many different pvalues. I'm attaching a screenshot of what the results look like. What could be the explanation here? Screen Shot 2024-01-11 at 3 00 39 PM

assaron commented 10 months ago

@johnse this is a normal behavior of Benjamini-Hochber correction for multiple testing, which is employed by fgsea. It's especially noticeable when there aren't many highly significant p-values, like in your case.