[BioC] GOstat question

[Robert Gentleman]

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
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org