[Bioc-devel] ath1121501 hyperGTest

Kaiyu Shen ks280007 at ohio.edu
Wed May 6 16:25:33 CEST 2009


Hi, folks:
I am now dealing with the ath1121501.db package and the hyperGTest in
GOStats. 
I have pulled out a list of genes, with their probe ID.
these genes are selected with their GO term available, and no
duplicates.
I tried:
params=new("GOHyperGParams",geneIds=gene.list,annotation="ath1121501",ontology="BP",
pvalueCutoff=0.05, conditional=FALSE,testDirection="over")
result=hyperGTest(params)

However,they give me an error message :

Error in get(mapName, Envir=pkgEnv,inherits=FALSE):
variable "ath1121501ENTREZID" was not found
Error in mget(probes,ID2EntrezID(datPkg)):
error in evaluating the argument 'envir' in selecting a method for
function 'mget'

I searched online, and found that someone said in ath1121501.db, the
ENTREZID equals to the ACCNUM,so I tried to directly assign the value
as:
ath1121501ENTREZID<-ath1121501ACCNUM

however, error message still pops out. 
Does anybody have a clue of how this could be solved??

Thanks again. 
Kyle.



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