Hi all, I'm relatively new to R/Bioconductor. I'm trying to map Affy's HGU133plus2 probesids with OperonID/EnsemblIDs Eg. OperonIDs H200007039 EnsemblIDs ENSG00000169678 Desc Linker for activation of T cells (36 kDa phospho-tyrosine adaptor protein) (pp36) (p36-38). DB website link http://omad.operon.com/human2/index.php Is there an environment for OperonIDs in the hgu133plus2 package? Eg. library(hgu133plus2) xx<-as.list(hgu133plus2OPERONID) myU133plus2probes<-xx[match(operonidsofinterest,xx)] If there isn't, could we build one? Thank You regards Julian Lee Bioinformatics Specialist National Cancer Center SIngapore

On Nov 14, 2007 2:57 AM, Julian Lee <julian at="" omniarray.com=""> wrote: > Hi all, > > I'm relatively new to R/Bioconductor. > > I'm trying to map Affy's HGU133plus2 probesids with OperonID/EnsemblIDs > > Eg. > OperonIDs > H200007039 These IDs are not really considered public identifiers. They are related to a particular microarray platform. > EnsemblIDs > ENSG00000169678 These IDs are public identifiers. > Desc > Linker for activation of T cells (36 kDa phospho-tyrosine adaptor protein) (pp36) (p36-38). > > DB website link > http://omad.operon.com/human2/index.php > > Is there an environment for OperonIDs in the hgu133plus2 package? No. > Eg. > library(hgu133plus2) > xx<-as.list(hgu133plus2OPERONID) > myU133plus2probes<-xx[match(operonidsofinterest,xx)] > > If there isn't, could we build one? You could, yes. However, Bioconductor probably will not, since Operon IDs are not public identifiers. I can only guess what your use case is, but I would suggest that you look into using the biomaRt package to map hgu133plus2 IDs to Ensembl gene ids. If I recall, Operon was designed against Ensembl genes. Then, you can use standard R functions like merge() and match() to map the hgu133plus2 probes to Operon probes using the common Ensembl gene ids. Sean