
I have done the analysis with DAVID but someone told me to do this kind of analysis. because he believes that if i randomly select 185 others genes among the 6000 i will have the same annotation results ....  

> Date: Mon, 4 Jun 2012 09:14:13 -0400
> Subject: Re: [BioC] Gene list annotation
> From: sdavis2@mail.nih.gov
> To: guest@bioconductor.org
> CC: bioconductor@r-project.org; flower_des_iles@hotmail.com
> 
> On Mon, Jun 4, 2012 at 9:09 AM, Fleur [guest] <guest@bioconductor.org> wrote:
> >
> > Hi,
> > I'm trying to measure the significance of my gene annotation list.
> > Gene list of interest is composed of 185 genes ( among 6000 genes).In a first step, i performed a GO term analysis but i would like to know if i could have the same result by chance.
> > My idea was to randomly select 185 genes from the 6000 genes ( 100 times for example) and annotate those list and see if i could have the same terms by chance ... But how calculate a pvalue for each term at each repetition of the permutation ? Any idea ?
> > Someone know a package which do this king of thing ?
> 
> GOstats, topGo, limma (roast, romer, and friends), and several others
> might be applicable.  You mentioned that you had done a "GO term
> analysis", so you may have already done this, depending on what you
> meant by that statement.
> 
> Sean
> 
> 
> > Thanks in advance for your help
> >
> >
> >
> >
> >  -- output of sessionInfo():
> >
> > R version 2.13.0 (2011-04-13)
> > Platform: i386-pc-mingw32/i386 (32-bit)
> >
> > locale:
> > [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
> > [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
> > [5] LC_TIME=French_France.1252
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > --
> > Sent via the guest posting facility at bioconductor.org.
> >
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