[BioC] FW: Gene list annotation

[Sean Davis]

On Mon, Jun 4, 2012 at 9:50 AM, Stéphanie haaaaaaaa
<flower_des_iles at hotmail.com> wrote:
>
> 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 ....
>

DAVID uses a fisher-exact-based statistic for computing the
probability of enrichment.  Did you get p-values from DAVID?  If so,
you may have already accomplished your task.  If not, you can use
DAVID to get such a result, but that is for another list....

Sean

>> Date: Mon, 4 Jun 2012 09:14:13 -0400
>> Subject: Re: [BioC] Gene list annotation
>> From: sdavis2 at mail.nih.gov
>> To: guest at bioconductor.org
>> CC: bioconductor at r-project.org; flower_des_iles at hotmail.com
>>
>> 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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