Hello, I have a affymetrix dataset (23 arrays) consisting of txt files from the MAS 5.0 algorithm (original cel files are unavailable). I would like to analyze the data using R and bioconductor, is there any package for starting with these txt files? Also, I would like to do a RMA type normalization, is there anyway to do such a multichip normalization (quantile) on the txt file data? Maurizio

Hi Maurizio, using the text files (I guess normalized data?) for downstream anlysis works. Assuming you already took the expression values out of the individual files and made one big expression file out of it you can even press the data into an exprSet xx<-read.table("yourdata.txt",sep="\t",header=T,row.names=1) gh<-new("exprSet",exprs=as.matrix(xx)) You can also just iterate over the files and then get the expression values out and bind them together to get to the same result. But as far as I know you can't unnormalize your data so that RMA is not available. Cheers, Bj?rn >Hello, > >I have a affymetrix dataset (23 arrays) consisting of txt files from >the MAS 5.0 algorithm (original cel files are unavailable). I would >like to analyze the data using R and bioconductor, is there any >package for starting with these txt files? Also, I would like to do a >RMA type normalization, is there anyway to do such a multichip >normalization (quantile) on the txt file data? > >Maurizio > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > >