You can do either library(mgu74av2.db) thedata <- select(mgu74av2.db, probes, "SYMBOL") or g <- getBM( c("affy_mg_u74av2", "mgi_symbol"), "affy_mg_u74av2", probes, mouse) But you should note that the two probes you list below are not from the chip you are using in your query. The probes you supply are from some version of the Mouse Genome 430 series. If I assume the 430 version 2: getBM( c("affy_mouse430_2", "mgi_symbol"), "affy_mouse430_2", probes,mart) affy_mouse430_2 mgi_symbol 1 1460645_at Chordc1 2 1460644_at Bckdk > select(mouse4302.db, probes, "SYMBOL") PROBEID SYMBOL 1 1460644_at Bckdk 2 1460645_at Chordc1 Best, Jim On Monday, September 09, 2013 10:31:35 AM, Gundala Viswanath wrote: > I have the following list of probes (from Mouse), > > 1460644_at > 1460645_at > > The longer list can be found here: http://dpaste.com/1371949/plain/ > What I want to do is to convert that name with HUGO gene symbol using > R. What's the way to do it? > > I tried this but failed > > __BEGIN__ > > library(biomaRt) > dat<-read.table("http://dpaste.com/1371949/plain/") > probes<-as.vector(as.matrix(dat)) > mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") > g = getGene( id = probes, type = "affy_mg_u74av2", mart = mouse) > show(g) > > __END__ > > It prints Ensembl gene id instead (e.g.ENSMUSG00000057666) > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

You can do either library(mgu74av2.db) thedata <- select(mgu74av2.db, probes, "SYMBOL") or g <- getBM( c("affy_mg_u74av2", "mgi_symbol"), "affy_mg_u74av2", probes, mouse) But you should note that the two probes you list below are not from the chip you are using in your query. The probes you supply are from some version of the Mouse Genome 430 series. If I assume the 430 version 2: getBM( c("affy_mouse430_2", "mgi_symbol"), "affy_mouse430_2", probes,mart) affy_mouse430_2 mgi_symbol 1 1460645_at Chordc1 2 1460644_at Bckdk > select(mouse4302.db, probes, "SYMBOL") PROBEID SYMBOL 1 1460644_at Bckdk 2 1460645_at Chordc1 Best, Jim On Monday, September 09, 2013 10:31:35 AM, Gundala Viswanath wrote: > I have the following list of probes (from Mouse), > > 1460644_at > 1460645_at > > The longer list can be found here: http://dpaste.com/1371949/plain/ > What I want to do is to convert that name with HUGO gene symbol using > R. What's the way to do it? > > I tried this but failed > > __BEGIN__ > > library(biomaRt) > dat<-read.table("http://dpaste.com/1371949/plain/") > probes<-as.vector(as.matrix(dat)) > mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") > g = getGene( id = probes, type = "affy_mg_u74av2", mart = mouse) > show(g) > > __END__ > > It prints Ensembl gene id instead (e.g.ENSMUSG00000057666) > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099