Hi Thomas, You can get GeneBank IDs, but they are jumbled together with other sorts of accessions inside of the ACCNUM mappings. If you just want all possible accessions, you can do it like this: prbs = c("8180408","8180388") egs = unlist2(mget(prbs, hugene10sttranscriptclusterENTREZID, ifnotfound=NA)) mget(egs, org.Hs.egACCNUM, ifnotfound=NA) ## OR a more tabular way: prbs = c("8180408","8180388") merge(toTable(hugene10sttranscriptclusterENTREZID[prbs]), toTable(org.Hs.egACCNUM)) Regardless of which method you use, the result is the same and will net you all the accessions for these genes. At this point, it is pretty easy to filter out the refseq IDs (for example) by grepping for "_". But please notice however that you want to use the ACCNUM mapping from org.Hs.eg to get this. This mapping is NOT the same as the ACCNUM mapping in your chip package. That is because the one in your chip package only holds accessions that were used to actually make the association between the transcript IDs and the Entrez Gene IDs in that package. This makes it conceptually a bit different from all the other mappings. In contrast, the one in org.Hs.eg holds all of the accessions that are affiliated with a given gene. Hope that this helps you, Marc On 01/13/2011 01:25 PM, Thomas Hampton wrote: > > library(hugene10sttranscriptcluster.db) > > > ls("package:hugene10sttranscriptcluster.db") > [1] "hugene10sttranscriptcluster" > [2] "hugene10sttranscriptclusterACCNUM" > [3] "hugene10sttranscriptclusterALIAS2PROBE" > [4] "hugene10sttranscriptclusterCHR" > [5] "hugene10sttranscriptclusterCHRLENGTHS" > [6] "hugene10sttranscriptclusterCHRLOC" > [7] "hugene10sttranscriptclusterCHRLOCEND" > [8] "hugene10sttranscriptcluster_dbconn" > [9] "hugene10sttranscriptcluster_dbfile" > [10] "hugene10sttranscriptcluster_dbInfo" > [11] "hugene10sttranscriptcluster_dbschema" > [12] "hugene10sttranscriptclusterENSEMBL" > [13] "hugene10sttranscriptclusterENSEMBL2PROBE" > [14] "hugene10sttranscriptclusterENTREZID" > [15] "hugene10sttranscriptclusterENZYME" > [16] "hugene10sttranscriptclusterENZYME2PROBE" > [17] "hugene10sttranscriptclusterGENENAME" > [18] "hugene10sttranscriptclusterGO" > [19] "hugene10sttranscriptclusterGO2ALLPROBES" > [20] "hugene10sttranscriptclusterGO2PROBE" > [21] "hugene10sttranscriptclusterMAP" > [22] "hugene10sttranscriptclusterMAPCOUNTS" > [23] "hugene10sttranscriptclusterOMIM" > [24] "hugene10sttranscriptclusterORGANISM" > [25] "hugene10sttranscriptclusterORGPKG" > [26] "hugene10sttranscriptclusterPATH" > [27] "hugene10sttranscriptclusterPATH2PROBE" > [28] "hugene10sttranscriptclusterPFAM" > [29] "hugene10sttranscriptclusterPMID" > [30] "hugene10sttranscriptclusterPMID2PROBE" > [31] "hugene10sttranscriptclusterPROSITE" > [32] "hugene10sttranscriptclusterREFSEQ" > [33] "hugene10sttranscriptclusterSYMBOL" > [34] "hugene10sttranscriptclusterUNIGENE" > [35] "hugene10sttranscriptclusterUNIPROT" > > Above, I note that GeneBank ids are not directly supported for my > chip. Darn. > > I am therefore using an online converter to map a list of GenBank > accessions to ENTREZ gene ids because it looks tricky to use > the entrezGeneByID function in annotate for a list of IDS. > > Ami I missing something? > > Best, > > Tom > > _______________________________________________ > 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