[BioC] Gene Ontologies exploration

[Marc Carlson]

Hi Jose,

Have you seen the GOstats package?  It supports an analysis similar to 
what I think you are describing.  You can read the vignette here:

http://www.bioconductor.org/packages/2.11/bioc/vignettes/GOstats/inst/doc/GOstatsHyperG.pdf


Let me know if you have questions.


   Marc



On 02/06/2013 10:16 AM, Jose M Garcia Manteiga wrote:
> Dear Biocs,
> I would like to produce pie charts or similar with percentage of genes associated to selected Gene Ontologies categories (or KEGG), preferable if I can choose the categories so that I can customise them using some search by keyword option.
> I would like to do it to compare the percentage of genes expressed in two different samples for the selected categories.
> I have explored Voronto (outside Bioc) and goProfiles and GeneAnswers, but I am not sure these are the best options.
> Thanks in advance
> Regards
> Jose
>
> ------------------------------------------------------------
> Jose M. Garcia Manteiga PhD
>
> Data analyst in Functional Genomics
> Center for Translational Genomics and Bioinformatics
> San Raffaele Scientific Institute
> Via Olgettina 58
> 20132 Milano
> Italy
>
> Office: +39 02 26434751
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor