[BioC] Affymetrix CEL files
James W. MacDonald
jmacdon at uw.edu
Tue Apr 30 22:39:44 CEST 2013
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
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