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List:       bioconductor
Subject:    Re: [BioC] Inconsistency in GOstats results after GO enrichment
From:       "Tony Chiang" <tchiang () fhcrc ! org>
Date:       2008-02-29 14:00:56
Message-ID: 52f663c40802290600l4b45e20eg501ec14ece0cf2be () mail ! gmail ! com
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Hi Chanchal,

In addition to the small example, please provide the list with your output
of sessionInfo(). This way, when we try to reproduce your example, we will
try to use the same version of software packages that you are using.

Cheers,
--Tony


On 2/29/08, James W. MacDonald <jmacdon@med.umich.edu> wrote:
>
> 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@biochem.mpg.de
> > Phone: (Office) +49 (0) 89 8578 2296
> >
> > Fax:(Office) +49 (0) 89 8578 2219
> > http://www.biochem.mpg.de/mann/
> > ===============================
> >
> >
> >
> >
> >       [[alternative HTML version deleted]]
> >
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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
> 734-647-5623
>
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