[BioC] How to deal with Affymetrix probe that map to multiple genes

[Mete Civelek]

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 at 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.

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