[BioC] topGO documentation / clarification

[Adrian Alexa]

Hi Mike,

your code look good and you should get the correct results.

did you read the package vignette? Your issues are explained there. If
you still have trouble understanding a specific section please let me
know.


Best regards,
Adrian



On Wed, Aug 11, 2010 at 3:56 PM, Mike Dewar <mike.dewar at columbia.edu> wrote:
> Hi,
>
> I've been trying to figure out the usage of topGO for situations where all you have is a list of interesting probesets, along with all the probesets on a microarray. My problems, which have been discussed on the biostar webpage, seem to have been around the specification of geneSel and allGenes. I have ended up not specifying geneSel at all (which would normally be some test to do with a p-value or other score) and to specify allGenes as a named factor, where the probeset is 1 if I consider it interesting, and 0 otherwise. In the code snippet below, `exprset` is an ExpressionSet object and `interesting_genes` is the list of probesets I find interesting.
>
> library(topGO)
> library(mogene10sttranscriptcluster.db)
> load('exprset')
> load('interesting_genes')
> all_genes <- rownames(exprs(exprset))
> # then make a factor that is 1 if the probeset is "interesting" and 0 otherwise
> geneList <- factor(as.integer (all_genes %in% interesting_genes))
> # name the factor with the probeset names
> names (geneList) <- allGenes
> # form the GOdata object
> GOdata <-new ("topGOdata",
>    ontology = "BP",
>    allGenes = geneList,
>    nodeSize = 5,
>    # annot, tells topGO to map from GO terms to "genes"
>    annot = annFUN.GO2genes,
>    # so annot then calls something to perform this mapping GO2genes,
>    # which is this from the mogene... library
>    GO2genes = as.list(mogene10sttranscriptclusterGO2PROBE)
> )
>
> My questions for the list are:
>
> 1) is this OK? Will the results I get from a Fisher Test be valid? They /seem/ fine.
> 2) if this is valid, would it be worth making it clearer in the topGO documentation? It is specified that allGenes should be a vector of strings, or a named numerical vector.
>
> Cheers,
>
> Mike Dewar
>
> - - -
> Dr Michael Dewar
> Postdoctoral Research Scientist
> Applied Mathematics
> Columbia University
> http://www.columbia.edu/~md2954/
>
>
>
>
>
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>
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