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Question: FDR control in conditional Hypergeometric test
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9.3 years ago by
United States
Hi all, I have a question about GOstats. When I do an non-conditional analysis (conditional = FALSE) something like: params <- new("GOHyperGParams", geneIds = myDEgenes, universeGeneIds = myUniverse, annotation = mychip, ontology = "BP", pvalueCutoff = 1.0, conditional = FALSE, testDirection = "over") hgCondOver <- hyperGTest(params) tmp<-summary(hgCondOver) and I want to control the FDR, I use: tmp$pFDR<-p.adjust(tmp$Pvalue,"fdr") since tmp contains all GO terms tested, and therefore I know exactly how many tests were done. When I use: params <- new("GOHyperGParams", geneIds = myDEgenes, universeGeneIds = myUniverse, annotation = mychip, ontology = "BP", pvalueCutoff = 1.0, conditional = TRUE, testDirection = "over") hgCondOver <- hyperGTest(params) tmp<-summary(hgCondOver) the conditioning will be done always because pvalueCutoff = 1.0, and I can still control the FDR as above. And finally the question. How can I do conditioning only in some of the case (e.g. pvalueCutoff = 0.05) but still be able to control the FDR or FWER for the tests that I am doing. Because if I use pvalueCutoff = 0.05, the tmp dataframe will contain only the terms with Pvalue less than 0.05. Thank you, Adi