Hi Iain, I also had problems with the org.Xx.eg.db packages and ended up making a package, AnnotationFuncs, for it. It handles mapping from one identifier to another (via the central identifier), using the data packages. I have included an example below. > library(AnnotationFuncs) > library(org.Hs.eg.db) > syms <- c('ACTB', 'TNF', 'TGFB1') > translate(syms, from=org.Hs.egSYMBOL2EG, to=org.Hs.egENSEMBL) $ACTB [1] "ENSG00000075624" $TNF [1] "ENSG00000204490" "ENSG00000206439" "ENSG00000223952" "ENSG00000228321" [5] "ENSG00000228849" "ENSG00000230108" "ENSG00000232810" $TGFB1 [1] "ENSG00000105329" Kind regards Stefan McKinnon H?j-Edwards Dept. of Molecular Biology and Genetics Ph.D. Fellow Aarhus University Blichers All? 20, Postboks 50 DK-8830 Tjele Tel.: +45 8715 7969 Tel.: +45 8715 6000 Email: Stefan.Hoj-Edwards at agrsci.dk Web: www.agrsci.dk -----Oprindelig meddelelse----- Message: 4 Date: Thu, 6 Oct 2011 12:50:41 +0100 From: Iain Gallagher <iaingallagher@btopenworld.com> To: bioconductor <bioconductor at="" stat.math.ethz.ch=""> Subject: [BioC] mapping through org.Xx.eg.db packages Message-ID: <1317901841.98063.YahooMailClassic at web86708.mail.ird.yahoo.com> Content-Type: text/plain; charset="utf-8" Dear List I wonder is someone could shed some light on the following. Given a set of gene symbols I would like to retrieve different identifiers. Using the org.Xx.eg.db packages I can go about this by mapping through the EntrezIDs: # mapping through eg ids as package is eg id centric library(org.Hs.eg.db) syms <- c('ACTB', 'TNF', 'TGFB1') egID <- unlist(mget(syms, org.Hs.egSYMBOL2EG, ifnotfound=NA)) ensID <- unlist(mget(egID, org.Hs.egENSEMBL, ifnotfound=NA)) > ensID 60 71241 71242 71243 "ENSG00000075624" "ENSG00000204490" "ENSG00000206439" "ENSG00000223952" 71244 71245 71246 71247 "ENSG00000228321" "ENSG00000228849" "ENSG00000230108" "ENSG00000232810" 7040 "ENSG00000105329" > egID ACTB TNF TGFB1 "60" "7124" "7040" Now here I assumed that the names of the ensID object were the original EntrezIDs mapped from the symbols but because R does not handle duplicate names they are not - with renumbering for those EntrezIDs that have a plurality of matches (here 7124 becomes 71241, 71242 etc etc) This has caused me some confusion since each of these names is an actual Entrez ID - just not one I'm interested in. The same can happen when mapping from any ID that ends in a numeric part (eg Ensembl ids). It is useful to return a mapping showing the original identifier, the EntrezID mapped through and the required identifier so how could one reliably do this when mapping through e.g. Entrez IDs as in the method above (i.e. return the Entrez ID and Ensembl ID in one sweep)? I have tried using the SQL approach: dbCon <- org.Hs.eg_dbconn() sqlQuery <- 'SELECT * FROM genes, gene_info, ensembl WHERE genes._id = gene_info._id = ensembl._id;' result <- dbGetQuery(dbCon, sqlQuery) where one could filter the 'result' object with the symbols of interest but this query takes a long time to run. I know little SQL so that might be an issue! Best iain