[BioC] Using Gostats on a new organism

[Marc Carlson]

Hello everyone,

If you cannot find a .db package for your model organism of choice, then
you might want to look at the vignette titled "Hypergeometric tests for
less common model organisms" in the GOstats package.  You can see this
vignette online right here:

http://www.bioconductor.org/packages/release/bioc/vignettes/GOstats/inst/doc/GOstatsForUnsupportedOrganisms.pdf


  Marc





On 06/15/2010 06:12 AM, January Weiner wrote:
> Many thanks to you both -- although I cannot directly use Biomart,
> both topGO and GOStats seem to be a viable alternative.
>
> Best regards,
>
> j.
>
> On Tue, Jun 15, 2010 at 12:31 PM, michael watson (IAH-C)
> <michael.watson at bbsrc.ac.uk> wrote:
>   
>> Hi
>>
>> This may not help you with GOstats, but we have example code on our website on how to use topGO:
>>
>> http://bioinformatics.iah.ac.uk/sample-code
>>
>> Thanks
>> Mick
>> ________________________________________
>> From: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] On Behalf Of January Weiner [january.weiner at mpiib-berlin.mpg.de]
>> Sent: 15 June 2010 11:19
>> To: BioC
>> Subject: [BioC] Using Gostats on a new organism
>>
>> Dear all,
>>
>> I am fighting with the GOStats vignettes and the corresponding
>> chapters from the Springer books, and I'm lost.
>>
>> I have a genome (and corresponding arrays) of an organism, along with
>> GO assignments. I'd like to run an enrichment analysis. GOStats seems
>> to need the db packages, is that correct? Is there another way of
>> running it?
>>
>> I would be grateful for any links or hints for further reading.
>>
>> Best regards,
>>
>> January
>>
>> P.S. I'd like to thank here for all who have helped me before; I don't
>> want to clutter the discussions with countless "thank you" e-mails :-)
>>
>> --
>> -------- Dr. January Weiner 3 --------------------------------------
>> Max Planck Institute for Infection Biology
>> Charitéplatz 1
>> D-10117 Berlin, Germany
>> Web   : www.mpiib-berlin.mpg.de
>> Tel     : +49-30-28460514
>>
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>>
>>     
>
>
>