I have an expression set where the featureNames are already human entrez ids. What annotation package should I use to run GSVA? I tried org.Hs.eg.db, but I get this error: > coad_es<-gsva(entrezSet, c2BroadSets, min.sz=10, max.sz=500, verbose=TRUE)$es.obs Mapping identifiers between gene sets and feature names Error in GeneSetCollection(lapply(what, mapIdentifiers, to, ..., verbose = verbose)) : error in evaluating the argument 'object' in selecting a method for function 'GeneSetCollection': Error in get(mapName, envir = pkgEnv, inherits = FALSE) : object 'org.Hs.egENTREZID' not found Am I doing something wrong?

On 03/04/2012 01:47 PM, Ed Siefker wrote: > I have an expression set where the featureNames are already human > entrez ids. What annotation package should I use to run GSVA? I > tried org.Hs.eg.db, but I get this error: > >> coad_es<-gsva(entrezSet, c2BroadSets, min.sz=10, max.sz=500, verbose=TRUE)$es.obs > Mapping identifiers between gene sets and feature names > Error in GeneSetCollection(lapply(what, mapIdentifiers, to, ..., > verbose = verbose)) : > error in evaluating the argument 'object' in selecting a method for > function 'GeneSetCollection': Error in get(mapName, envir = pkgEnv, > inherits = FALSE) : > object 'org.Hs.egENTREZID' not found Hi Ed -- Actually, I think this is related to a bug report on the Bioc-devel mailing list the other day https://stat.ethz.ch/pipermail/bioc-devel/2012-February/003151.html https://stat.ethz.ch/pipermail/bioc-devel/2012-March/003173.html and a work-around is to create a self-map org.Hs.egENTREZID = new.env(hash=TRUE, parent=emptyenv()) for (k in keys(org.Hs.egENSEMBL)) org.Hs.egENTREZID[[k]] = k The underlying issue is fixed in GSEABase available with R-2.15 alpha, to be released at the end of the month. Martin > > > Am I doing something wrong? > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793