Hi all,

I was wondering if anybody could give me pointers on how to use GOstats with
a custom list of gene annotations/categories
I have my list of yeast genes associated with one or more of 25 different
categories

My file looks something like this:

Gene_A Category_1
Gene_A Category_2
Gene_B Category_1
Gene_B Category_2
Gene_C Category_2
Gene_C Category_3

I am not sure how to convert this into an annotation that GOstats likes.
I tried to figure out how to do it using the AnnotationDbi library, but I
wasn't able to so any pointers would be greatly appreciated.

My current GOstats command is
params=new("GOHyperGParams",geneIds=sel,universeGeneIds=uni,annotation="org.Sc.sgd.db",ontology=class,pvalueCutoff=as.numeric(pvalue),conditional=FALSE,testDirection="over")
    over=hyperGTest(params)

Thanks,

Iain

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