[BioC] GSEABase how to map gene symbols to mouse EntrezId or Affy

Marc Carlson mcarlson at fhcrc.org
Thu May 15 18:26:35 CEST 2008

Vladimir Morozov wrote:
> Hi
> Any suggestions how to map  gene symbols to mouse EntrezId(preffered) or
> Affy. 
> mapping to Entez apparently is not supported by GSEABase
Hi Vladimir,

In general if you want to map mouse gene symbols to Entrez Gene IDs, I 
would use the org.Mm.eg.db package like this:
#load the package

#you need a some gene symbols to map of course
foo = c("Msx2", "Wnt5a", "Shh")

#Then just find what these symbols map to
mget(foo, org.Mm.egSYMBOL2EG)

If you have more exotic gene symbols in your list (often many symbols 
will map to a single ID), then you can also use the org.Mm.egALIAS2EG 
mapping to try and recover the gene IDs that may have otherwise been lost.

And if you want to map to affy IDs, we probably have a package for that 
too, but you need to tell us which platform you are using in order for 
us to make a recommendation.


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