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2.8 years ago
I have 3 groups (control, treated 1, treated 2) for which I obtained log fold changes between the different conditions and would like to run GSEA to compare all of them (so that I can get themes that are enriched in each of the conditions). Would I just have to consider them pairwise? More importantly, would I have to correct for multiple hypothesis testing?
Compare them in terms of what? GSEA-like analysis compares a given ranked dataset (e.g. DE results from control vs treated1 ranked by fold change) with a gene set, e.g. a hallmark set of a disease or any other gene set you can think of. For pairwise comparisons between samples one does pairwise DE, e.g. with DESeq2. Please clarify.
@ATpoint Edited the question