Hi,

I was trying to find if a cluster of genes were 'significant', and was using the hyperGTest function provided in GOstats. I am reproducing the code and the error below:
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> selGenes
[1] "YCL019W" "YCL020W" "YER160C" "YJR026W" "YJR028W" "YML045W"
> class(selGenes)
[1] "character"
>     library("GOstats")
>     library("YEAST")
>     set.seed(434)    
>     allYeast <- ls(YEASTCHR)
> p <- new("GOHyperGParams",
+              geneIds=selGenes,
+              universeGeneIds=allYeast,
+              ontology="BP",
+              annotation="YEAST",
+              pvalueCutoff=0.05,
+              testDirection="over",
+              conditional=FALSE)
>     ans <- hyperGTest(p)
Error in order(na.last, decreasing, ...) : 
        argument 1 is not a vector
> 

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For most of my clusters, I don't get errors. I suspect it is something to do with the genes in this particular cluster. If I put the same genes in sgd (http://db.yeastgenome.org/cgi-bin/GO/goTermFinder), and test them with the default gene universe (i.e the full complement of yeast genes), I don't get an error.

Am I doing something wrong?

many thanks!

PS: The code above is a slight modification to the code used by Seth Falcon to one of my earlier queries.

       
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