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Hi Simone -- I've found it convenient to take the M and A matrices and 'flatten' them into a data frame, along the lines of > M <- matrix(rnorm(10000), ncol=5) > A <- matrix(rnorm(10000), ncol=5) > colnames(M) <- colnames(A) <- LETTERS[1:5] > df <- data.frame(Samp=rep(colnames(M), each=nrow(M)), > M=as.vector(M), > A=as.vector(A)) and then use lattice to display the results > library(lattice) > xyplot(M~A|Samp, df) > library(geneplotter) > xyplot(M~A|Samp, df, panel=panel.smoothScatter) > xyplot(M~A|Samp, df, panel=function(...) { > panel.smoothScatter(...) > panel.abline(0,0) > }) Martin "Simone de Jong" <s.dejong-6 at="" umcutrecht.nl=""> writes: > I am using the Lumi package to analyze my Illumina expression data (mouse). > > I was wondering whether there is a user friendly way to construct an > aggregate sample to plot my samples against in MA plots, instead of plotting > them in a pairwise manner. > > > > Thanks, > > > > Simone de Jong, Msc. > > PhD student > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793