[BioC] topGO documentation / clarification
adrian.alexa at gmail.com
Wed Aug 11 23:31:06 CEST 2010
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
On Wed, Aug 11, 2010 at 3:56 PM, Mike Dewar <mike.dewar at columbia.edu> wrote:
> 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.
> 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.
> Mike Dewar
> - - -
> Dr Michael Dewar
> Postdoctoral Research Scientist
> Applied Mathematics
> Columbia University
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