[BioC] Converting Affymetrix (*_at) Mouse Probe ID to HUGO gene symbol

[James W. MacDonald]

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)
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099