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

[James W. MacDonald]

I have just pushed a fix for this to the release repository, so it looks 
like GOstats will ship with a fixed version of probeSetSummary().

Note that this function still doesn't work exactly as I would like - the 
vector of 'selected' identifiers only counts one probeset per Entrez 
Gene ID because of the necessity to subset to unique Entrez Gene IDs 
before doing the hyperGTest(). The devel version now has an additional 
argument 'sigProbesets' that can be used to overcome this limitation, 
but we are well past the point that changes to the API can be introduced 
to release packages so this will have to wait for release 2.1 (and those 
who like to live on the bleeding edge with devel packages).

Best,

Jim

James W. MacDonald wrote:
> 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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