Question: Affymetrix CEL files
0
gravatar for Stephanie M. Gogarten
6.6 years ago by
University of Washington
Stephanie M. Gogarten740 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) 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 >
cdf gwastools • 1.4k views
ADD COMMENTlink modified 6.6 years ago by James W. MacDonald51k • written 6.6 years ago by Stephanie M. Gogarten740
Answer: Affymetrix CEL files
0
gravatar for James W. MacDonald
6.6 years ago by
United States
James W. MacDonald51k 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) 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 > 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
ADD COMMENTlink written 6.6 years ago by James W. MacDonald51k
Answer: Affymetrix CEL files
0
gravatar for James W. MacDonald
6.6 years ago by
United States
James W. MacDonald51k wrote:
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/pr imer.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
ADD COMMENTlink written 6.6 years ago by James W. MacDonald51k
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
ADD REPLYlink written 6.6 years ago by Benilton Carvalho4.3k
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