Hello, I am trying to obtain a GeneSetCollection (package GSEABase) corresponding to an experiment using the hgu95a annotation. When I use for example, the KEGG gene set collection, the mapping and creation of the GeneSetCollection object takes place without issue: gsc <- GeneSetCollection(eset, setType=KEGGCollection()) On the other hand when I enter: > gsc <- GeneSetCollection(eset, setType=PfamCollection()) I get: Error in `direction<-`(`*tmp*`, value = -1L) : changing the direction of an "IpiAnnDbMap" object is not supported Similarly for: > gsc <- GeneSetCollection(eset, setType=ChrlocCollection()) I get: Error in `direction<-`(`*tmp*`, value = -1L) : changing the direction of an "AnnDbMap" object is not supported Is there any help that anyone can give me for how to correct this issue? Here is some version information, in case it matters: platform powerpc-apple-darwin8.11.1 arch powerpc os darwin8.11.1 system powerpc, darwin8.11.1 status major 2 minor 8.0 year 2008 month 10 day 20 svn rev 46754 language R version.string R version 2.8.0 (2008-10-20) Thanks, James Wagner [[alternative HTML version deleted]]

Hi James -- James Wagner <jamesrwagner at="" gmail.com=""> writes: > Hello, I am trying to obtain a GeneSetCollection (package GSEABase) > corresponding to an experiment using the hgu95a annotation. > > When I use for example, the KEGG gene set collection, the mapping and > creation of the GeneSetCollection object takes place without issue: > > gsc <- GeneSetCollection(eset, setType=KEGGCollection()) > > On the other hand when I enter: > >> gsc <- GeneSetCollection(eset, setType=PfamCollection()) > > I get: > > Error in `direction<-`(`*tmp*`, value = -1L) : > changing the direction of an "IpiAnnDbMap" object is not supported > > Similarly for: > >> gsc <- GeneSetCollection(eset, setType=ChrlocCollection()) > > I get: > > Error in `direction<-`(`*tmp*`, value = -1L) : > changing the direction of an "AnnDbMap" object is not supported These are definitely shortcomings in GSEABase, and I'll work to get a fix in place over the next couple of days. Martin > Is there any help that anyone can give me for how to correct this issue? > > Here is some version information, in case it matters: > > platform powerpc-apple-darwin8.11.1 > arch powerpc > os darwin8.11.1 > system powerpc, darwin8.11.1 > status > major 2 > minor 8.0 > year 2008 > month 10 > day 20 > svn rev 46754 > language R > version.string R version 2.8.0 (2008-10-20) > > Thanks, > > James Wagner > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793