I'm a bit confused about gene set enrichment analysis:
In this review they classify GSEA as a "functional class scoring method (FCS)" (table 1) whereas in the book "The Biostar Handbook" literally says: "Gene set enrichment analysis can be performed in several ways. One of the most commonly used is approach is the over-representation analysis (ORA)" (page 241).
I understand that gene set enrichment analysis is a method to find over-represented genes from a previous-ranqued list (obtained by FCS). In other words, to make a gene set enrichment analysis you need a FCS + ORA, am I off track?.
Does the review i mentioned earlier refer to a software called GSEA that performs both analysis?
Thanks in advance!
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I think the confusion may stem from the fact that the Broad Institute's
GSEAtool uses a specific way of testing for enrichment of entire classes/sets of genes, which is not ORA, but "functional class scoring" in the terms of the review you're citing. The main difference between the methods is captured by neither nomenclature, IMO. The techniques that Khatri et al refer to as "ORA" basically just compare the absence/presence of single genes or gene sets between two lists (think Venn diagrams) whereas the FCS techniques refer to methods that try to take more information into account, such as the ranking of one of the lists.The ranking is not determined by FCS. FCS needs a ranked list of your genes of interest to determine whether the genes that are at the top/bottom of your list are more likely to be present in the gene sets that are to be assessed for overrepresentation.
Confusingly, there is additionally an ORA analysis tool available on the GSEA website: https://www.gsea-msigdb.org/gsea/msigdb/annotate.jsp
This question is answered, for that reason I close the question.