[BioC] GOstat question
Nicolas.Servant at curie.fr
Thu Mar 20 21:28:54 CET 2008
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 :
Pvalue = 0.04
OddsRatio = 0.04
ExpCount = 11
Count = 17
Size = 45
But, when i did the opposite :
entrez <- unique(unlist(mget(as.vector(unlist(test)),hgu133plus2ENTREZID)))
I don't understand why I find 126 entrez IDs in the Universe, and no 45
as expected (SIZE) ...
In the same way, I find 50 entrez IDs in my list, and no 17 as expected
Thanks for your explanations,
26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE
Email: Nicolas.Servant at curie.fr
Tel: 01 53 10 70 55
More information about the Bioconductor