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Fast Gene Set Enrichment Analysis
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Does fGSEA require minSize as well? #130

Closed MEladawi closed 1 year ago

MEladawi commented 1 year ago

Hi--

I wanted to inquire if fGSEA Monte Carlo based p-value also requires minSize of 15-25 like the original GSEA to prevent the p-value inflation? or we can use it with smaller sets?

Best,

assaron commented 1 year ago

We don't have any hard data, but we do recommend to set certain minSize value (may be incorrectly). I usually use 15, but occasionally use lower values for some pathway collections, when there are potentially interesting gene sets of small size. Otherwise small gene sets frequently have high non-significant nominal P-value, which decreases the overall power due to Benjamini-Hochber multiple hypotheses testing correction.