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

[James MacDonald]

>>> "Henrik Bengtsson" <hb at stat.berkeley.edu> wrote:
> 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

Wow! And I thought gas prices have gone through the roof. I think you were only charging $0.02 just yesterday.

Maybe we need a senate inquiry into price gouging by HB?

;-P

Jim


> 
> 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 
>> **************************************************************
>>
>> 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.
>>
>> This e-mail message is confidential and for use by the a...{{dropped:2}}
>>
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