[BioC] CGH-like workflow for Affymetrix SNP 500k

[Daniel Brewer]

Hello,

I have recently got a bunch of Affymetrix SNP 500k CEL files that I
would like to analyse.  I haven't done any work  on SNP arrays before
but have done a fair amount of aCGH stuff.  What I would like to be able
to do is apply something like DNAcopy to the data and be able to
visualise and export where there are amplifications etc..  Currently, I
am not concerned with the allele stuff.

Could anyone give me an example workflow to do this and what packages
they used.

Many thanks

-- 
**************************************************************
Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
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The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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