Converting Affymetrix (*_at) Mouse Probe ID to HUGO gene symbol
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@gundala-viswanath-2872
Last seen 7.1 years ago
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)
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@gundala-viswanath-2872
Last seen 7.1 years ago
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)
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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
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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
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