Hi all, I am trying to make a M vs. A plot of an array. I don't know how to get my data in the correct format for the MAplot command in affy. How do I get my data in the correct format after Data <- ReadAffy()? Any help is appreciated. Thanks! Kanan

kvyas wrote: > Hi all, > > I am trying to make a M vs. A plot of an array. I don't know how to get my > data in the correct format for the MAplot command in affy. How do I get my > data in the correct format after Data <- ReadAffy()? Any help is appreciated. Your data *is* in the correct format at this point. You should be able to simply do MAplot(Data) to get the MA plot(s). Note that this function plots each chip versus a pseudo-median chip, so it may not be what you are expecting. If you want MA plots for all possible comparisons, you should use the mva.pairs() function. Note that this function expects a matrix of data, so you will have to first extract the PM or MM data using the pm() accessor function. mva.pairs(pm(Data)) HTH, Jim > > Thanks! > > Kanan > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109

Thanks! I will give that a try. Kanan >===== Original Message From "James W. MacDonald" <jmacdon@med.umich.edu> ===== >kvyas wrote: >> Hi all, >> >> I am trying to make a M vs. A plot of an array. I don't know how to get my >> data in the correct format for the MAplot command in affy. How do I get my >> data in the correct format after Data <- ReadAffy()? Any help is appreciated. > >Your data *is* in the correct format at this point. You should be able >to simply do > >MAplot(Data) > >to get the MA plot(s). Note that this function plots each chip versus a >pseudo-median chip, so it may not be what you are expecting. If you want >MA plots for all possible comparisons, you should use the mva.pairs() >function. Note that this function expects a matrix of data, so you will >have to first extract the PM or MM data using the pm() accessor function. > >mva.pairs(pm(Data)) > >HTH, > >Jim > >> >> Thanks! >> >> Kanan >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > >-- >James W. MacDonald >Affymetrix and cDNA Microarray Core >University of Michigan Cancer Center >1500 E. Medical Center Drive >7410 CCGC >Ann Arbor MI 48109