James W. MacDonald | 8 Oct 15:27 2012

Re: Illumina SNP array annotation

Hi Fabrice,

On 10/6/2012 2:10 PM, Fabrice Tourre wrote:
> When I analysis Illumina 5M SNP array data, I found some SNP name is
> strange to me. e.g. kgp12193496, kgp9527405.

Those are 1000Genomes SNPs (kgp = 1000 Genomes Project). They can be 
fairly difficult to annotate - your best bet is to extract the chr/pos 
information from the Illumina annotation file and then use those data to 
map to rs IDs.

Best,

Jim

>
> Is there bioconductor can search for the annotation? I know lots of
> expression array anotation on bioconductor, but I cannot find
> annotation for SNP array.
>
> Thank you.
>
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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

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