[BioC] Converting to official gene symbols

[James MacDonald]

I think the OP wants to map aliases to official gene symbols rather than 
mapping affy probe ids to symbols.

Something like this should work:

 > library(org.Hs.eg.db)
 > eg <- get("GAB", org.Hs.egALIAS2EG)
 > symb <- get(eg, org.Hs.egSYMBOL)
 > symb
[1] "A1BG"

You can also do these things directly using sql statements if 
interested, see the AnnotationDbi vignette for examples.

Best,

Jim



Gundala Viswanath wrote:
> Hi,
> 
> 
>>> Is there a function available on Bioconductor to convert gene symbol
>>> aliases to official gene symbols?
> 
> 
> Yes. Is this you what you are looking for?
> 
> 
>> source('http://bioconductor.org/biocLite.R')
>> biocLite() # installs a number of pacakges
>> biocLite('hgu95av2.db') # a particular chip 'annotation' file
>> library(hgu95av2.db)
>> hgu95av2GENENAME[["1053_at"]]
> [1] "replication factor C (activator 1) 2, 40kDa"
>> hgu95av2SYMBOL[["1053_at"]]
> [1] "RFC2"
> 
> Further option can be found here:
>> help(package=hgu95av2.db)
> 
> and
> 
>> openVignette()
> 
> 
> - G.V.
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>>
>> --
>> Kang Tu
>>
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-- 
James W. MacDonald, MS
Biostatistician
UMCCC cDNA and Affymetrix Core
University of Michigan
1500 E Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623