[BioC] GOstat question

[nicolas servant]

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/