[BioC] GOstats hyperGTest( ): Counts of EntrezIDs returned from summary() are not same as the numbers of EntrezIDs extracted from probeSetSummary()

[James W. MacDonald]

Seth Falcon wrote:
> Hi Jim,
> 
> Any insight on this one?
> 
> "Na, Ren" <Na at uthscsa.edu> writes:
> 
>>Hi, I tried to find the genes in some of significant GO categories,
>>and find out Counts of EntrezIDs returned from summary() are not
>>same as the numbers of entrezIDs extracted from probeSetSummary()
>>for some significant GO categories. My question is whether they
>>should be same.  Here is the code I used,

They should be the same - you have uncovered a bug.

This function works perfectly well if conditional = FALSE, but if you 
condition then the simple way we are mapping from Entrez Gene IDs ==> 
Probeset IDs no longer works, because we are ignoring the fact that the 
number of Entrez Gene IDs under consideration at any level of the GO DAG 
is conditional upon any significant child terms.

Right now we are in the final stages of releasing BioC 2.0, so the 
GOstats package will almost certainly be released with this bug intact. 
However, I will be working to correct the problem and will push any 
fixes to the release repository.

I will send a note to this list when the fix is in. The version will 
also increment, so a simple

library(Biobase)
update.packages(repos = biocReposList())

should get things updated when that happens.

Best,

Jim





-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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