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!






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