[BioC] Affymetrix CEL files

[James W. MacDonald]

Hi Hugo,

Strike that. You just want the oligo package. The crlmm package is for 
estimating copy number, not calling SNPs. See e.g., 
http://bioconductor.org/packages/2.12/bioc/vignettes/oligo/inst/doc/primer.pdf, 
starting on p. 18.

Best,

Jim



On 4/30/2013 4:36 PM, Hugo Loyola wrote:
> Thank you Jim, my data is SNP6 Affymetrix
>
> Hugo
>
>
> On Tue, Apr 30, 2013 at 4:33 PM, James W. MacDonald <jmacdon at uw.edu 
> <mailto:jmacdon at uw.edu>> wrote:
>
>     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
>         <mailto: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
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099