[BioC] Affymetrix CEL files

[James W. MacDonald]

Hi Hugo,

You need to specify what type of Affymetrix celfiles you have. You would 
likely use e.g. the crlmm or oligo package, but it depends on what 
genotyping array you are using. If you are using the 5.0 or 6.0 series, 
then you would want to use crlmm, otherwise likely oligo.

Best,

Jim



On 4/30/2013 4:20 PM, Stephanie M. Gogarten wrote:
> Dear Hugo,
>
> You are correct that you will need to do some pre-processing of the 
> CEL files before you can use GWASTools.  GWASTools begins with called 
> genotypes in plain text format, and the vignettes can help you convert 
> from plain text into NetCDF for use with the GWASTools functions.
>
> I don't have any experience with calling genotypes from CEL format, 
> but I suspect you might want to use the "oligo" package.  This page 
> gives you an outline of options:
> http://www.bioconductor.org/help/workflows/oligo-arrays/#pre-processing-resources 
>
>
> Hopefully someone on this list who is familiar with CEL files can give 
> you additional comments.  If you have follow-up questions, please copy 
> the bioconductor mailing list (bioconductor at r-project.org) and use an 
> informative subject line.
>
> best wishes,
> Stephanie
>
> On 4/30/13 12:55 PM, Hugo Loyola wrote:
>> Dear Stephanie Gogarten, my name is Hugo and I want to apply the
>> GWASTools package on a series of Affymetrix CEL files. I already see the
>> vignette related with this type of data format but I think that I will
>> need more information. Do you know of another source where to look at?
>> This is the first time that I need to perform this type of analysis so I
>> feel unsecure on how to proceed.
>>
>> For example, I need to read the cel files with some package, previous to
>> make available for data proccesing?
>>
>> Thank you, in advance, for your time and pardon me for this irruption
>>
>> Hugo Loyola
>> Escuela de Medicina
>> Universidad del Desarrollo
>>
>
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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