Discarding probes that map to multiple unique gene symbols would be my suggestion. There is no way to know which gene expression the probeset is measuring. -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Gundala Viswanath Sent: Monday, September 09, 2013 10:46 PM To: bioconductor at stat.math.ethz.ch; bioconductor at r-project.org Subject: [BioC] How to deal with Affymetrix probe that map to multiple genes Given a (e.g.431765_a_at), I'm trying to find the gene symbol. But some how it gives multiple genes. How can I interpret that properly? This is the example code and output: library(biomaRt) mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") getBM( c("affy_mouse430_2", "mgi_symbol"),mart=mouse, filters="affy_mouse430_2", "1431765_a_at") Which yields: affy_mouse430_2 mgi_symbol 1 1431765_a_at Rps2-ps13 2 1431765_a_at Gm12176 3 1431765_a_at Gm7860 4 1431765_a_at Gm12366 5 1431765_a_at Gm10653 6 1431765_a_at Rps2-ps4 7 1431765_a_at Gm10420 8 1431765_a_at Rps2 9 1431765_a_at Gm5921 10 1431765_a_at Gm15846 11 1431765_a_at Gm16061 12 1431765_a_at Gm6433 13 1431765_a_at Gm4968 14 1431765_a_at Gm9013 15 1431765_a_at Gm17150 16 1431765_a_at Gm11687 17 1431765_a_at Gm18025 18 1431765_a_at Gm8225 19 1431765_a_at Gm11643 20 1431765_a_at Gm11249 21 1431765_a_at Gm12922 22 1431765_a_at Gm12933 23 1431765_a_at Gm16148 24 1431765_a_at Gm6139 25 1431765_a_at Gm5786 26 1431765_a_at Rps2-ps9 27 1431765_a_at Gm11599 28 1431765_a_at Gm16305 29 1431765_a_at 4931440P22Rik 30 1431765_a_at Gm12091 31 1431765_a_at Gm6311 32 1431765_a_at Rps2-ps6 33 1431765_a_at Rps2-ps10 34 1431765_a_at Gm5070 35 1431765_a_at Snora64 In reality, having multiple probe set, I'd convert all the affymetrix ID into gene symbol. And later perform clustering, GO analysis, etc based on these genes. Your expert advice will be much appreciated. - G.V. _______________________________________________ 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 ________________________________ IMPORTANT WARNING: This email (and any attachments) is o...{{dropped:9}}

Discarding probes that map to multiple unique gene symbols would be my suggestion. There is no way to know which gene expression the probeset is measuring. -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Gundala Viswanath Sent: Monday, September 09, 2013 10:46 PM To: bioconductor at stat.math.ethz.ch; bioconductor at r-project.org Subject: [BioC] How to deal with Affymetrix probe that map to multiple genes Given a (e.g.431765_a_at), I'm trying to find the gene symbol. But some how it gives multiple genes. How can I interpret that properly? This is the example code and output: library(biomaRt) mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") getBM( c("affy_mouse430_2", "mgi_symbol"),mart=mouse, filters="affy_mouse430_2", "1431765_a_at") Which yields: affy_mouse430_2 mgi_symbol 1 1431765_a_at Rps2-ps13 2 1431765_a_at Gm12176 3 1431765_a_at Gm7860 4 1431765_a_at Gm12366 5 1431765_a_at Gm10653 6 1431765_a_at Rps2-ps4 7 1431765_a_at Gm10420 8 1431765_a_at Rps2 9 1431765_a_at Gm5921 10 1431765_a_at Gm15846 11 1431765_a_at Gm16061 12 1431765_a_at Gm6433 13 1431765_a_at Gm4968 14 1431765_a_at Gm9013 15 1431765_a_at Gm17150 16 1431765_a_at Gm11687 17 1431765_a_at Gm18025 18 1431765_a_at Gm8225 19 1431765_a_at Gm11643 20 1431765_a_at Gm11249 21 1431765_a_at Gm12922 22 1431765_a_at Gm12933 23 1431765_a_at Gm16148 24 1431765_a_at Gm6139 25 1431765_a_at Gm5786 26 1431765_a_at Rps2-ps9 27 1431765_a_at Gm11599 28 1431765_a_at Gm16305 29 1431765_a_at 4931440P22Rik 30 1431765_a_at Gm12091 31 1431765_a_at Gm6311 32 1431765_a_at Rps2-ps6 33 1431765_a_at Rps2-ps10 34 1431765_a_at Gm5070 35 1431765_a_at Snora64 In reality, having multiple probe set, I'd convert all the affymetrix ID into gene symbol. And later perform clustering, GO analysis, etc based on these genes. Your expert advice will be much appreciated. - G.V. _______________________________________________ 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 ________________________________ IMPORTANT WARNING: This email (and any attachments) is o...{{dropped:9}}