[BioC] Affymetrix CEL files

[Benilton Carvalho]

If it's Affy SNP 5/6, I'd suggest the crlmm package, which has a
faster and improved implementation of our genotype calling algorithm
(compared to what is available in oligo).

http://www.bioconductor.org/packages/release/bioc/vignettes/crlmm/inst/doc/genotyping.pdf

b

2013/4/30 James W. MacDonald <jmacdon at uw.edu>:
> 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
>>
>>
>>         _______________________________________________
>>         Bioconductor mailing list
>>         Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>>
>>         https://stat.ethz.ch/mailman/listinfo/bioconductor
>>         Search the archives:
>>         http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>>     --     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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor