[BioC] Probe include snp in HG-U133_Plus_2

[James W. MacDonald]

Hi Fabrice,

On 2/12/2012 11:41 PM, Fabrice Tourre wrote:
> Dear list,
>
> I am doing HG-U133_Plus_2 data analysis.
> In my data analysis, I want to get the probe list which include
> SNP(the snp is defined in 1000Genome). So first, I want to the probe
> genome position in U133_Plus_2 array. I have checked in this page
> (http://www.affymetrix.com/support/technical/byproduct.affx?product=hg-u133-plus).
> But it seems I can not find a suitable file.

You could use the BSgenome package for this. See

http://bioconductor.org/packages/release/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf

in particular the last section.

Best,

Jim


>
> Any suggestions would be greatly appreciated :)
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099