Hi, Edward Bolanger <ebolanger at="" yahoo.com=""> writes: > I was trying to find if a cluster of genes were 'significant', and > was using the hyperGTest function provided in GOstats. I am > reproducing the code and the error below: > -------------------------------------------------------------------- -------------------------------------------- >> selGenes > [1] "YCL019W" "YCL020W" "YER160C" "YJR026W" "YJR028W" "YML045W" >> class(selGenes) > [1] "character" >> library("GOstats") >> library("YEAST") >> set.seed(434) >> allYeast <- ls(YEASTCHR) Hmm, it doesn't look like any of selGenes are in your universe. I get: selGenes %in% allYeast [1] FALSE FALSE FALSE FALSE FALSE FALSE > >> p <- new("GOHyperGParams", > + geneIds=selGenes, > + universeGeneIds=allYeast, > + ontology="BP", > + annotation="YEAST", > + pvalueCutoff=0.05, > + testDirection="over", > + conditional=FALSE) >> ans <- hyperGTest(p) > Error in order(na.last, decreasing, ...) : > argument 1 is not a vector That isn't such a helpul error message, but it also isn't the one I get: p <- new("GOHyperGParams", + geneIds=selGenes, + universeGeneIds=allYeast, + ontology="BP", + annotation="YEAST", + pvalueCutoff=0.05, + testDirection="over", + conditional=FALSE) Error in makeValidParams(.Object) : no geneIds in universeGeneIdsFALSE In addition: Warning message: removing geneIds not in universeGeneIds in: makeValidParams(.Object) [Now this one looks like it could use some improvement as well, but the no geneIds in uverseGeneIds part is actually fairly helpful I think] > For most of my clusters, I don't get errors. I suspect it is > something to do with the genes in this particular cluster. If I put > the same genes in sgd > (http://db.yeastgenome.org/cgi-bin/GO/goTermFinder), and test them > with the default gene universe (i.e the full complement of yeast > genes), I don't get an error. Presumably things work better when the genes you have selected are in your universe of genes... + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org