[BioC] problem with hyperGTest function
sfalcon at fhcrc.org
Tue Jun 5 16:50:57 CEST 2007
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Andrzej Polański <Andrzej.Polanski at polsl.pl> writes:
> I am really enthusiastic about your implementation of hypergeometric
> tests to problems in GO analyses. I have been working on it for a
> couple of weeks. I was so happy when I found your GOstats package
> within Bioconductor. Since I am not an expert on R (I do my analyses
> using Matlab), I am experiencing some problems with your hyperGtest
> function. Below please find an exemplary code:
First of all, have you read over the vignette that comes with GOstats?
Try this if you have not:
## then select 1 which should open a PDF viewer for you
> affySample <- c("204724_s_at", "214349_at", "205054_at", "209875_s_at", "205700_at");
> geneSample <- as.vector(unlist(mget(affySample, hgu133aACCNUM, ifnotfound=NA)));
You want to use EntrezGene identifiers to define the selected gene
list and the gene universe. So you want:
geneSample <- unlist(mget(affySample, hgu133aENTREZID))
## but should still filter out NA's, etc
> affyUniverse <- ls(hgu133acdf);
You don't need the hgu133acdf package for this. If you want to use as
your universe all genes probed on the chip, then you can do:
chipEntrezUniverse <- as.list(hgu95av2ENTREZID)
chipEntrezUniverse <- unique(unlist(chipEntrezUniverse))
But you really do not, IMHO, want to use all the genes on the entire
chip as your universe (read through the vignette for why).
You can also save yourself a lot of effort by using the nsFilter
function to do the non-specific filtering of your data.
> geneUniverse <- as.vector(unlist(mget(affyUniverse, hgu133aACCNUM, ifnotfound=NA)));
> params <- new("GOHyperGParams", geneIds = geneSample, universeGeneIds = geneUniverse, annotation="hgu133a", ontology = "BP", pvalueCutoff = 0.9, conditional = FALSE, testDirection = "over");
> It works fine till that. Then, when I run:
> hgOver <- hyperGTest(params);
> The following error appears:
> Error in getUniverseHelper(probes, datPkg, entrezIds) :
> No Entrez Gene ids left in universe
Note that the error happens during the call to hyperGTest, not the
call to summary().
> Could you, please, tell me, what is wrong?
You haven't given the right IDs.
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
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