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ctlab / fgsea

Fast Gene Set Enrichment Analysis
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fgsea-simple vs fgsea-multilevel - when to use one or the other? #103

Closed mgrantpeters closed 2 years ago

mgrantpeters commented 3 years ago

Hello, thank you for the great package. I wondered whether you could explain in more detail the difference of applicability of fgsea-simple vs fgsea-multilevel - in particular, in your paper you describe “Here we present a fast gene set enrichment analysis (FGSEA) method for efficient estimation of GSEA P-values for a collection of pathways. The method consist of two main procedures: FGSEA-simple and FGSEA-multi-level. FGSEA-simple procedure allows to efficiently estimate P-values with a limited accuracy but simultaneously for the whole collection of gene sets, while FGSEA-multilevel procedure allows to accurately estimate arbitrarily low P-values but for individual gene sets.” What do you mean by gene sets in this case? Does this refer to gene sets obtained from a previous step (e.g.: differential expression), gene sets from GO, KEGG, etc databases or something else entirely?

assaron commented 3 years ago

Hi, sorry about the confusion: in the manuscript FGSEA-multilevel refers to the particular algorithm of calculating low P-values for individual gene sets (as individual pathways from GO/KEGG/etc), while fgseaMultilevel() function in the package combines both FGSEA-simple and FGSEA-multilevel procedures in an efficient manner. So you should use fgseaMultievel(), fgseaSimple() was left for compatibility purposes.