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Yoder, Sean J. wrote: > I'm trying to perform density plots on members on a MAS 5 expression set > derived from 5 .cel files, but I'd like to plot "present", "absent', and > "marginal" genes in distinct plots...all on the same graphics pane. > > > > I suppose I first need to combine my MAS data with my MAS calls, then > for each array, create filtered matrices based on the PMA calls. Then I > could use plotDensity() to display them. Can someone give me some > pointers from here? I can't seem to get cbind() to combine my data and > my calls together to even get started and a search of the archives was > fruitless. > > > > dat <- ReadAffy() > > eset.mas5 <- mas5(dat) > > eset.mas5.calls <- mas5calls(dat) > > # need to combine these No, you don't need to combine anything. > > # need to filter by P,M,A > > # need to call plotDensity() You won't be able to use plotDensity() because it expects a matrix, and it is doubtful that you will have equal numbers of genes for each sample. Better to just call plot(density()). I am sure that this could be done in a much cleaner manner, but as a first attempt, this should work. plot(density(exprs(eset.mas5)), type = "n") ## make a blank plot for(i in 1:5){ index <- exprs(eset.mas5.calls)[,i] == "P" lines(density(exprs(eset.mas5)[index,i]), lty=1, col=1) index <- exprs(eset.mas5.calls)[,i] == "M" lines(density(exprs(eset.mas5)[index,i]), lty=2, col=2) index <- exprs(eset.mas5.calls)[,i] == "A" lines(density(exprs(eset.mas5)[index,i]), lty=3, col=3) } You might have to add a ylim argument to the first plot() call to make sure the y-axis is the correct length. Best, Jim > > > > Thank you, > > > > Sean > > > > Sean Yoder, M.S. > > Research Associate > > Microarray Core Facility > > Moffitt Cancer Center & Research Institute > > E-mail: yodersj at moffitt.usf.edu > > Fax: 813-979-7265 > > Phone: 813-745-1917 > > > > > > > > > ----------------------------------------- > #################################################################### ####### > ## This transmission may be confidential or protected from disclosure and > is only for review and use by the intended recipient. Access by anyone else > is unauthorized. Any unauthorized reader is hereby notified that any > review, use, dissemination, disclosure or copying of this information, or > any act or omission taken in reliance on it, is prohibited and may be > unlawful. If you received this transmission in error, please notify the > sender immediately. Thank you. ######################################### > #################################### > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at 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 734-647-5623