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

[Henrik Bengtsson]

Hi,

see the aroma.affymetrix package
(http://groups.google.com/group/aroma-affymetrix/).  There is an
online Vignette 'Total copy number analysis (10K, 100K, 500K)' doing
what you want at

   http://groups.google.com/group/aroma-affymetrix/web/total-copy-number-analysis

My $100,000

Cheers

Henrik

On Fri, Jun 20, 2008 at 3:19 AM, Daniel Brewer <daniel.brewer at icr.ac.uk> wrote:
> 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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