Answer: Inconsistency in GOstats results after GO enrichment
11.6 years ago by
Unless you can give us a small reproducible example that shows what
are talking about, there is really nothing anybody can do about this.
Chanchal Kumar wrote:
> Dear All,
> I have been using the "GOstats" package for the GO enrichment on
> 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
> I get "Cell Cycle" (GO:0007049) as enriched. Till there it's fine.
> strangely I see that the Category Size ( "Size" column of the output
> gives me different numbers for Cell cycle annotated genes in my
> set( in test1 77, in test2 366). Now my concern is that given I use
> 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 Kumar, Ph.D. Candidate
> Dept. of Proteomics and Signal Transduction
> Max Planck Institute of Biochemistry
> Am Klopferspitz 18
> 82152 D-Martinsried (near Munich)
> e-mail: chanchal at biochem.mpg.de
> Phone: (Office) +49 (0) 89 8578 2296
> Fax:(Office) +49 (0) 89 8578 2219
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
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