Hi Marc, Yes, the organism would be homo sapiens. ----- Original Message ---- From: Marc Carlson To: Paul Evans Cc: Bioconductor@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! > > > > > > > ____________________________________________________________________________________ > Looking for last minute shopping deals? > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Do you know what organism are the data from? Marc ____________________________________________________________________________________ Looking for last minute shopping deals? [[alternative HTML version deleted]]