[BioC] Using Gostats on a new organism

[Heidi Dvinge]

Hello January,

GOstats mostly use the db packages, but it's also possible to use it  
without, as long as you have you own gene-to-GO mappings (can be  
downloaded from e.g. Ensembl vis biomaRt in many cases). Have a look  
at the vignette "GOstatsForUnsupportedOrganisms.pdf"  at  http:// 
www.bioconductor.org/packages/release/bioc/html/GOstats.html

HTH
\Heidi

On 15 Jun 2010, at 11:31, michael watson (IAH-C) 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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