the following should work for you, assuming you've got enough RAM: theCalls = calls(object)[] final = theCalls for (i in 1:3) final[theCalls == i] = c('AA', 'AB', 'BB')[i] b On 18 July 2012 10:04, Pina Iannelli <pina.iannelli at="" gmail.com=""> wrote: > Dear Benilton, thanks for your help! > When I try your code, I get this error: > > Error in as.hi.integer(x, maxindex = maxindex, dim = dim, vw = vw, pack = > pack) : > NAs in as.hi.integer > In addition: Warning message: > In `[<-.ff_array`(`*tmp*`, theCalls == i, value = "AA") : > opening ff > C:/Users/Pina/Bioinformatica/SNP/COR354_SNP6/call-9201fc1496a.ff > > And then when I use write.table function I get this error: > > Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = > stringsAsFactors) : > cannot coerce class 'c("ff_matrix", "ff_array", "ff")' into a data.frame > > Can you help me? thanks a lot! > Pina > > 2012/7/13 Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> >> >> there is a calls() accessor that will return you the calls as integers >> (1: AA; 2: AB; 3: BB). So, something along the lines of: >> >> theCalls = calls(object) >> final = theCalls >> for (i in 1:3) >> final[theCalls == i] = c('AA', 'AB', 'BB')[i] >> >> Then it's just a matter of using write.table() to write out the file >> using the "final" object. >> >> b >> >> On 13 July 2012 11:22, Pina Iannelli <pina.iannelli at="" gmail.com=""> wrote: >> > Dear all, >> > I run this code to get genotyping from Affymetrix SNP 6.0 arrays: >> > >> > fullFilenames <- >> > list.celfiles("C:/Users/Pina/Bioinformatica/SNP/COR354_SNP6", full.names >> > = >> > TRUE) >> > outputDir <- file.path(getwd(), "crlmmResults") >> > exampleSet <- genotype(fullFilenames, batch = rep("1", 2), cdfName = >> > "genomewidesnp6", gender=c(1, 2)) >> > >> > Now I nead to ha ve a file with genotyping information, such as: >> > >> > SNP_A-1780270 BB BB AA SNP_A-1780272 BB AB BB >> > How can I do it? >> > Thanks for your help, best regards >> > Pina >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > 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 > >