[BioC] Affymetrix CEL files

[Stephanie M. Gogarten]

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
>