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 

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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@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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