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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