[BioC] Gene list annotation

[Sean Davis]

On Mon, Jun 4, 2012 at 9:09 AM, Fleur [guest] <guest at 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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