Dear list, I would like to carry out a Gene Set Analysis on the KEGG pathways on my Human Gene ST 1.0 array experiment using GSEABase. The annotation data included in this experiment is pd.hugene.1.0.st.v1, but it hasn't got functions like pd.hugene.1.0.st.v1PATH2PROBE. These functions are handled by hugene10sttranscriptcluster.db, so, my idea was to, first, using hugene10sttranscriptclusterENTREZID to get the entrezID for each gene in the experiment and then call GeneSetCollection using these entrezIDs, something like that: GeneSetCollection(entrezIDlist, idType="EntrezIdentifier",setType=KEGGCollection()), but it doesn't work Error en function (classes, fdef, mtable) : unable to find an inherited method for function "GeneSetCollection", for signature "character", "character", "KEGGCollection" How can I build my Gene set object? Thanks, Javier

Hi Javier -- Javier P?rez Florido <jpflorido at="" gmail.com=""> writes: > Dear list, > I would like to carry out a Gene Set Analysis on the KEGG pathways on > my Human Gene ST 1.0 array experiment using GSEABase. The annotation > data included in this experiment is pd.hugene.1.0.st.v1, but it hasn't > got functions like pd.hugene.1.0.st.v1PATH2PROBE. These functions are > handled by hugene10sttranscriptcluster.db, so, my idea was to, first, > using hugene10sttranscriptclusterENTREZID to get the entrezID for each > gene in the experiment and then call GeneSetCollection using these > entrezIDs, something like that: > > GeneSetCollection(entrezIDlist, > idType="EntrezIdentifier",setType=KEGGCollection()), but it doesn't > work > Error en function (classes, fdef, mtable) : > unable to find an inherited method for function "GeneSetCollection", > for signature "character", "character", "KEGGCollection" Are you looking for something like the following from the help page for GeneSetCollection? ## from KEGG identifiers, for example library(KEGG.db) lst <- head(as.list(KEGGEXTID2PATHID)) gsc <- GeneSetCollection(mapply(function(geneIds, keggId) { GeneSet(geneIds, geneIdType=EntrezIdentifier(), collectionType=KEGGCollection(keggId), setName=keggId) }, lst, names(lst))) but perhaps with lst <- head(as.list(KEGGEXTID2PATHID)) replaced by lst <- as.list(KEGGEXTID2PATHID[entrezIDlist]) Martin > > How can I build my Gene set object? > Thanks, > Javier > > _______________________________________________ > 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 M1 B861 Phone: (206) 667-2793