[BioC] GO classification

[Thomas Girke]

GO_Slim categories are usually sets of very general custom GO terms. Examples of these
GO_Slim sets can be downloaded from geneontology.org:
	http://www.geneontology.org/GO.slims.shtml

When working with GOstats, you can simply use your favorite GO_Slim set for subsetting 
your enrichment analysis results and then plot the corresponding counts. Usually, GO_Slim
representations, especially pie charts, pretend that the different items (e.g. genes) are 
assigned to only one category - which is typically not the case - since there are duplicates 
almost everywhere. 

As a suggestion to the developers:
Considering the popularity of these GO_Slim representations, it might be useful to add some 
instructions in the GOstats PDF that illustrate to users how to generate counts and plots 
for their favorite GO_Slim categories? Perhaps with a proper warning about the limitations of
these analyses.

Best,

Thomas


On Wed 10/10/07 11:23, Celine Carret wrote:
> Hi, 
> you should have a look at this:
> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/goSlim.t
> xt
> 
> I found it very clear, and useful, and if you don't work on human-chips
> you can customise the script easily.
> 
> Best regards
> Celine
> 
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Ganiraju
> Sent: 09 October 2007 20:37
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] GO classification
> 
> hi,
> 
> I got a set of  significant GOids by running my data using GOhypergtest
> of
> Gostats. Now im trying to classify these GO ids using the GO_slim
> classifier. Is there any package in R which can accomplish this job??
> 
> Thanks
> Gani
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Thomas Girke
Assistant Professor of Bioinformatics
Director, IIGB Bioinformatic Facility
Center for Plant Cell Biology (CEPCEB)
Institute for Integrative Genome Biology (IIGB)
Department of Botany and Plant Sciences
1008 Noel T. Keen Hall
University of California
Riverside, CA 92521

E-mail: thomas.girke at ucr.edu
Website: http://faculty.ucr.edu/~tgirke
Ph: 951-827-2469
Fax: 951-827-4437