
Hi Robert,

Thanks for the reply and the helpful advice. I looked at some of the functions in GOstats and these are perhaps the ones
that I need. Specifically, I am trying to use the 'HyperGTest' function. 
I was looking at the document titled 'How To Use GOstats
Testing Gene Lists for GO Term Association' to setup a new instance of 'GoHyperGParam'. The documentation says:'If you
are using the YEAST annotation package, the vector will consist of FIXME.' I'm not quite sure what I should put here. I tried using systemic names (e.g YER111C) for yeast genes
but got the following error message:

> params <- new("GOHyperGParams", geneIds = clust2,
+         universeGeneIds = allGenes2, annotation = "YEAST",
+          ontology = "BP", pvalueCutoff = hgCutoff, conditional = FALSE,
+          testDirection = "over")
>   hgOver <- hyperGTest(params)   
Error in getUniverseHelper(probes, lib, entrezIds) : 
        No Entrez Gene ids left in universe


Which ids/names should I be using for Yeast? 

many thanks !

>
>
>
>
>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!
> 
>  

 
---------------------------------
8:00? 8:25? 8:40?  Find a flick in no time

	[[alternative HTML version deleted]]

