Hi Andrzej, [I'm sending a copy to the bioconductor list. Please send further questions about GOstats to the Bioconductor list so others can benefit from the answers and chime in with suggestions] Andrzej Pola?ski <andrzej.polanski at="" polsl.pl=""> writes: > I am really enthusiastic about your implementation of hypergeometric > tests to problems in GO analyses. I have been working on it for a > couple of weeks. I was so happy when I found your GOstats package > within Bioconductor. Since I am not an expert on R (I do my analyses > using Matlab), I am experiencing some problems with your hyperGtest > function. Below please find an exemplary code: > First of all, have you read over the vignette that comes with GOstats? Try this if you have not: openVignette(package="GOstats") ## then select 1 which should open a PDF viewer for you > library(hgu133a); > affySample <- c("204724_s_at", "214349_at", "205054_at", "209875_s_at", "205700_at"); > geneSample <- as.vector(unlist(mget(affySample, hgu133aACCNUM, ifnotfound=NA))); You want to use EntrezGene identifiers to define the selected gene list and the gene universe. So you want: geneSample <- unlist(mget(affySample, hgu133aENTREZID)) ## but should still filter out NA's, etc > library(hgu133acdf); > affyUniverse <- ls(hgu133acdf); You don't need the hgu133acdf package for this. If you want to use as your universe all genes probed on the chip, then you can do: chipEntrezUniverse <- as.list(hgu95av2ENTREZID) chipEntrezUniverse <- unique(unlist(chipEntrezUniverse)) But you really do not, IMHO, want to use all the genes on the entire chip as your universe (read through the vignette for why). You can also save yourself a lot of effort by using the nsFilter function to do the non-specific filtering of your data. > geneUniverse <- as.vector(unlist(mget(affyUniverse, hgu133aACCNUM, ifnotfound=NA))); > params <- new("GOHyperGParams", geneIds = geneSample, universeGeneIds = geneUniverse, annotation="hgu133a", ontology = "BP", pvalueCutoff = 0.9, conditional = FALSE, testDirection = "over"); > > It works fine till that. Then, when I run: > > hgOver <- hyperGTest(params); > summary(hgOver); > > The following error appears: > > Error in getUniverseHelper(probes, datPkg, entrezIds) : > No Entrez Gene ids left in universe Note that the error happens during the call to hyperGTest, not the call to summary(). > Could you, please, tell me, what is wrong? You haven't given the right IDs. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org