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