[BioC] Gene Ontology - Finding Significant terms

[Robert Gentleman]

Why not simply use GOstats, or one of the many other GO related 
Bioconductor packages and do the analysis entirely in R?

But if you don't want to do that then RCurl has some tools that will 
allow you to interact with FORMS based interfaces, and some of the 
examples in that package may help to point you to a software solution.

best wishes
   Robert


Edward Bolanger wrote:
> Hi,
> 
> I am doing some clustering on a set of yeast genes. To evaluate the quality of the clusters, I take the genes in a cluster and test them at SGD website:
> 
> http://db.yeastgenome.org/cgi-bin/GO/goTermFinder
> 
> Essentially, I upload the genes in the cluster (Step 1), and the set of background genes (Step 3). This then gives me a GO graph indicating whether the cluster is significant or not.
> 
> I would like to have some automated process that uploads the clusters and saves the webpages with the results, since I would like to test many clusters. The SGD website itself hits AMIGO.
> 
> Is there any package that will let me do this? Or any other possible ideas of how I may go about doing this? Preferably, I should be able to call this from inside R code.
> 
> many thanks!
> 
>  
> ---------------------------------
> We won't tell. Get more on shows you hate to love
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org