I've had success with GWASTools and Affy SNP 6.0. The GWASTools authors have written a detailed tutorial that describes their approach to data cleaning and quality control. It can be found here: http://www.bioconductor.org/packages/release/bioc/vignettes/GWASTools/ inst/doc/DataCleaning.pdf Cheers, Fred On 6/3/12 6:04 PM, Vincent Carey wrote: > There are various ways of proceeding. For calling with crlmm, an example > of a full analysis is given with > > http://www.bioconductor.org/packages/2.10/bioc/vignettes/crlmm/inst/ doc/gtypeDownstream.pdf > > be sure to look at > > http://www.bioconductor.org/packages/2.10/bioc/html/crlmm.html > > GWASTools should also be consulted. > > On Sun, Jun 3, 2012 at 6:52 PM, David Hervás<ddhervas@yahoo.es> wrote: > >> Hello, >> >> I'm new to Bioconductor and after searching and reading lots of >> documentation files from different packages I still haven't figured how to >> perform GWAS with Affymetrix SNP 6.0 arrays >> As far as I know I need "oligo", "pd.genomewidesnp.6" and "snpStats" >> pacakages but I haven't found an example of how to put all the commands >> together. >> >> >> I've managed to read my .CEL files with the following code provided in the >> oligo package documentation: >> >> setwd("d:\\CELS\\") >> fullFilenames<- list.celfiles(full.names=TRUE) >> outputDir<- file.path(getwd(), "crlmmResults") >> >> if (!file.exists(outputDir)) crlmm(fullFilenames, outputDir) >> >> crlmmOut<- getCrlmmSummaries(outputDir) >> >> >> I get a SnpSuperSet object, and I also know how to get the genotypes from >> it with >> >> genotype<-calls(crlmmOut) >> >> What are the next steps to perform the association analysis? Documentation >> in oligo package suggests "snpStats" but I have no idea how to make this >> package read my SnpSuperSet object or my genotype matrix, since snpStats >> needs a SNPmatrix object. I've also tried other packages but none seem to >> be able to read SnpSuperSet objects. >> >> Thanks in advance for you help >> >> >> ________________ >> David Hervás Marín >> Biostatistician in IIS La Fe - Valencia >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

Thanks for the links! The example in the first link seems to be just what I was looking for. ________________ David Hervás Marín Biostatistician in IIS La Fe - Valencia ________________________________ De: Vincent Carey <stvjc@channing.harvard.edu> Para: David Hervás <ddhervas@yahoo.es> CC: "bioconductor@r-project.org" <bioconductor@r-project.org> Enviado: Lunes 4 de junio de 2012 1:04 Asunto: Re: [BioC] GWAS with Affymetrix SNP 6.0 There are various ways of proceeding.  For calling with crlmm, an example of a full analysis is given with http://www.bioconductor.org/packages/2.10/bioc/vignettes/crlmm/inst/do c/gtypeDownstream.pdf be sure to look at http://www.bioconductor.org/packages/2.10/bioc/html/crlmm.html GWASTools should also be consulted. On Sun, Jun 3, 2012 at 6:52 PM, David Hervás <ddhervas@yahoo.es> wrote: Hello, > >I'm new to Bioconductor and after searching and reading lots of documentation files from different packages I still haven't figured how to perform GWAS with Affymetrix SNP 6.0 arrays >As far as I know I need "oligo", "pd.genomewidesnp.6" and "snpStats" pacakages but I haven't found an example of how to put all the commands together. > > >I've managed to read my .CEL files with the following code provided in the oligo package documentation: > >setwd("d:\\CELS\\") >fullFilenames <- list.celfiles(full.names=TRUE) >outputDir <- file.path(getwd(), "crlmmResults") > >if (!file.exists(outputDir)) crlmm(fullFilenames, outputDir) > >crlmmOut <- getCrlmmSummaries(outputDir) > > >I get a SnpSuperSet object, and I also know how to get the genotypes from it with > >genotype<-calls(crlmmOut) > >What are the next steps to perform the association analysis? Documentation in oligo package suggests "snpStats" but I have no idea how to make this package read my SnpSuperSet object or my genotype matrix, since snpStats needs a SNPmatrix object. I've also tried other packages but none seem to be able to read SnpSuperSet objects. > >Thanks in advance for you help > > >________________ >David Hervás Marín >Biostatistician in IIS La Fe - Valencia > >_______________________________________________ >Bioconductor mailing list >Bioconductor@r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]