Hi all,

I was wondering if somebody could point me in the right direction. I would
like to use GOSlim from the SGD
website<ftp://genome-ftp.stanford.edu/pub/yeast/data_download/literature_curation/>with
the GOStats package, but I am not sure how to change the
ontology/annotation.

I am currently using the following set of commands to do my Go analysis.
library(GOstats)
library("org.Sc.sgd.db")
x <- org.Sc.sgdGENENAME  #To generate the set of gene names
mapped_genes <- mappedkeys(x)
sel<-mapped_genes[1:10]   #selected set of genes
uni<-mapped_genes           #universe of genes
params=new("GOHyperGParams",geneIds=sel,universeGeneIds=uni,annotation="org.Sc.sgd.db",ontology="BP",pvalueCutoff=0.05,conditional=FALSE,testDirection="over")
over=over=hyperGTest(params)

Thanks for any help,

Iain

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