Paul Evans wrote: > Hi Marc, > > Yes, the organism would be homo sapiens. > > > > > ----- Original Message ---- > From: Marc Carlson <mcarlson at="" fhcrc.org=""> > To: Paul Evans <p.evans48 at="" yahoo.com=""> > Cc: Bioconductor at stat.math.ethz.ch > Sent: Wednesday, March 26, 2008 12:05:20 PM > Subject: Re: [BioC] Newbie question on GOstats (hyperGTest) for dual > channel (from SMD) arrays > > Paul Evans wrote: > > Hi, > > > > I had a microarray dataset (dual channel taken from Stanford > Microarray Database) of 20,000 genes. I have used a filtering > technique to reduce this to about 2500 genes. I now want to perform > clustering and use the hyperGTest, as given in the GOstats: > > > > hgCutoff <- 0.001 > > params <- new("GOHyperGParams", geneIds = selectedEntrezIds, > > universeGeneIds = entrezUniverse, annotation = "hgu95av2", > > ontology = "BP", pvalueCutoff = hgCutoff, conditional = FALSE, > > testDirection = "over") > > > > > > I understand that the universeGeneIds will be the entrez ids of the > 2500 genes, and that the selectedEntrezIds are the entrez ids of the > genes in a cluster, but what should I choose as the annotation > package? I don't think the SMD gives the details of the array that was > used. > > > > many thanks! > > > > > Then I would try to use the org.Hs.eg.db package. This package provides annotations for all the entrez gene IDs in Homo sapiens. Marc