[BioC] GOstat question

[nicolas servant]

Sorry. I use the BioC GOStats package (2.2.6).
In connection with my last mail, I have a other question :

##universe
designALL<-names(unlist(as.list(hgu133plus2ACCNUM)))
entrezUniverse <- 
na.omit(unique(unlist(mget(designALL,hgu133plus2ENTREZID))))
##myList
selectedEntrezIds <- 
na.omit(unique(unlist(mget(mylist,hgu133plus2ENTREZID))))
params.BP.over<-new("GOHyperGParams",geneIds=selectedEntrezIds,universeGeneIds=entrezUniverse,annotation="hgu133plus2",ontology="BP",pvalueCutoff=0.05,conditional=TRUE,testDirection="over")
params.MF.over<-new("GOHyperGParams",geneIds=selectedEntrezIds,universeGeneIds=entrezUniverse,annotation="hgu133plus2",ontology="MF",pvalueCutoff=0.05,conditional=TRUE,testDirection="over")
params.CC.over<-new("GOHyperGParams",geneIds=selectedEntrezIds,universeGeneIds=entrezUniverse,annotation="hgu133plus2",ontology="CC",pvalueCutoff=0.05,conditional=TRUE,testDirection="over")

hgOver.BP<-hyperGTest(params.BP.over)
hgOver.MF<-hyperGTest(params.MF.over)
hgOver.CC<-hyperGTest(params.CC.over)

length(selectedEntrezIds)
[1] 3761
length(hgOver.BP at geneIds)
[1] 3122

I guess the hyperGTest has removed these 639 missing genes. But i don't 
understand why ?

Nicolas

Robert Gentleman a écrit :
> Hi Nicolas,
>
>    Perhaps you could peruse the posting guide and provide the 
> information it asks you to.  Only from that could one hope to give you a 
> reasonable answer (ie, what commands did you run, what what the output, 
> and your sessionInfo, at a bare minimum).  And the Bioconductor package 
> is GOstats, not GOstat - that is something else (not Bioconductor) and 
> if you want help with it you should ask those folks directly.
>
>   Robert
>
>
> nicolas servant wrote:
>   
>> Hi,
>>
>> I have a question about the GOstat package.
>> I'm working with a list of probesets, and i'm interested by testing the 
>> over representation of the GO terms in my list.
>> So, I changed the probesets IDs (of my lists and my Universe) into 
>> ENTREZ IDs and the hyperGTest performed well.
>> For instance i have some result as :
>>
>> GO:0005635
>> Pvalue = 0.04
>> OddsRatio = 0.04
>> ExpCount =  11
>> Count = 17
>> Size = 45
>>
>> But, when i did the opposite :
>>
>> test<-mget("GO:0005635",hgu133plus2GO2ALLPROBES)
>> entrez <- unique(unlist(mget(as.vector(unlist(test)),hgu133plus2ENTREZID)))
>> length(entrez)
>> [1] 126
>>
>> I don't understand why I find 126 entrez IDs in the Universe, and no 45 
>> as expected (SIZE) ...
>>
>> mylistentrez<-unique(intersect(entrez,mylist))
>> length(mylistentrez)
>> [1] 50
>>
>> In the same way, I find 50 entrez IDs in my list, and no 17 as expected 
>> (COUNT)
>>
>> Thanks for your explanations,
>> Bests,
>>
>> Nicolas
>>
>>     
>
>   


-- 
Nicolas Servant
Equipe Bioinformatique
Institut Curie
26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE

Email: Nicolas.Servant at curie.fr
Tel: 01 53 10 70 55
http://bioinfo.curie.fr/