Hi,

I was trying the hyperGTest function and used this simple script:

---------------------------------- 
> library("hgu95av2")
> library(GOstats)
> 
> chip <- "hgu95av2"
> hgCutoff <- 0.2
> ont <- "BP"
> 
> xx <- as.list(hgu95av2ENTREZID)
> # Remove probe identifiers that do not map to any ENTREZID
> xx <- xx[!is.na(xx)]
> if(length(xx) > 0){
+      # The ENTREZIDs for the first two elements of XX
+      xx[1:2]
+      # Get the first one
+      xx[[1]]
+ }
[1] "652"
> 
> allEntrez <- unlist(xx)
> 
> geneSet <- allEntrez[1:50]
 
> params <- new("GOHyperGParams", geneIds = geneSet,
+              universeGeneIds = allEntrez, annotation = "hgu95av2", ontology = ont,
+              pvalueCutoff = hgCutoff, conditional = FALSE, testDirection = "over")
> 
> hgOver <- hyperGTest(params) 
Error: value for 'GO:0032650' not found
> 
-------------------------------------------------------------

I feel that I am making some very elementary mistake, but can't quite put my finger on it. Any hints/documentation that would steer me in the right direction?

thanks.




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