[BioC] Extract genes for a GO term in GOstat

James W. MacDonald jmacdon at med.umich.edu
Thu Jun 3 15:03:08 CEST 2010

Hi Rohit,

Rohit Farmer wrote:
> Hi everyone i did a GO enrichment analysis using GOstat package for around
> 112 genes and got 80 go terms enriched in BP ontology ... but the results
> are not showing what are the genes that are associated with a particular GO
> term ... command used are as followd
> library("hgu133plus2.db")
> allg <- get("hgu133plus2ENTREZID")
> allg <- as.data.frame(unlist(as.list(allg)))
> entrez.ids <- unique(allg[rownames(dat.s),])
> params <- new("GOHyperGParams", geneIds=entrez.ids,
> annotation=c("hgu133plus2"), ontology="BP", pvalueCutoff=0.05,
> conditional=FALSE, testDirection="over")
> resultBP<-hyperGTest(params)

probesets <- probeSetSummary(resultBP)

See ?probeSetSummary for more info.



> please help to find out the genes associated with the go terms
> Rohit

James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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