[BioC] Inconsistency in GOstats results after GO enrichment

[James W. MacDonald]

Hi Chanchal,

Unless you can give us a small reproducible example that shows what you 
are talking about, there is really nothing anybody can do about this.

Best,

Jim



Chanchal Kumar wrote:
> Dear All,
> 
>  
> 
>    I have been using the "GOstats" package for the GO enrichment on my
> dataset. I have two cluster of genes(test1, test2) and a reference
> set(universe set). After doing enrichment on the two sets for GO BP
> w.r.t to the universe set I get a list of enriched terms. In both cases
> I get "Cell Cycle" (GO:0007049) as enriched. Till there it's fine. But
> strangely I see that the Category Size ( "Size" column of the output )
> gives me different numbers for Cell cycle annotated genes in my universe
> set( in test1 77, in test2 366). Now my concern is that given I use the
> same universe set how I can get different numbers of Cell cycle
> annotated universe genes? This is just one example and I see these
> inconsistencies for many common terms. 
> 
>  
> 
> Any insights on this problem will be very helpful. 
> 
>  
> 
> Best Regards,
> 
> Chanchal 
> 
> ===============================
> 
> Chanchal Kumar, Ph.D. Candidate
> 
> Dept. of Proteomics and Signal Transduction
> Max Planck Institute of Biochemistry
> Am Klopferspitz 18
> 82152 D-Martinsried (near Munich)
> Germany
> e-mail: chanchal at biochem.mpg.de
> Phone: (Office) +49 (0) 89 8578 2296
> 
> Fax:(Office) +49 (0) 89 8578 2219
> http://www.biochem.mpg.de/mann/
> ===============================
> 
>  
> 
> 
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> 
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-- 
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
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