When use enricher function or GSEA of clusterProfiler R
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6 weeks ago
Will • 0

Hi, what is the differences between GSEA and enricher function of the R-clusterProfiler package? For e.g. after finding a set of DE genes through an RNA analysis on count data, it should be better to use GSEA or enricher function ?

GSEA enricher genes enrichment clusterProfiler • 188 views
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Entering edit mode
6 weeks ago
h.mon 32k

enrichr() performs a hypergeometric test comparing the set of "significant" genes against the "universe" (or background) genes. GSEA() is a Komolgorov-Smirnov test on the whole ranked gene list, testing if some category (e.g., a KEGG pathway) is more abundant at the top of the list than expected by chance. GSEA is generally considered preferable, as 1) it is considered more sensitive in general, as it can detect small, but concerted expression changes, and 2) it doesn't need the somewhat subjective step of defining which are the "significant" genes.