This is a perfect example why it is better to send to the list instead of me ;-D Jenny Drnevich wrote: > > See ?plotMA3by2 - I use it quite often, because it makes MA plots of > all your arrays all on the same scale, puts 6 per page, and downloads > the resulting files into your working directory. > > Cheers, > Jenny > > At 08:33 AM 9/12/2006, James W. MacDonald wrote: > >> Hi Yanju, >> >> Please don't send questions directly to me. Using the BioC list is >> preferred for at least two reasons. First, there are many people on the >> BioC list who might have a better answer for your question. Second, the >> list is archived and available for people to search, and your question >> and any resulting answer may help someone in the future. >> >> yanju wrote: >> > Dear James, >> > >> > In analyse of DNA microarray using LIMMA, for example: >> > targets<-readTargets("target.txt") >> > >> rg<-read.maimages(targets$FileName,source="genepix",wt.fun=wtflags( 0.1)) >> > >> > when I plot rg by using: >> > plotMA(rg) >> > Only one array has been plotted, but actually, I have 8 arrays . I >> tried >> > plotMA(rg, array=8), it did not work neither. >> > I want to know how to plot MA imagin of multiple arrays. >> > Expectin your reply. Thank you in advance. >> >> As far as I know, plotMA() is only designed to plot one array at a time. >> If you want to plot all the arrays, you have several choices. >> >> 1.) Plot all together in one window >> >> layout(matrix(1:8, nc = 2, byrow = TRUE)) >> for(i in 1:8) plotMA(rg, array = i) >> >> 2.) Make individual plots and save in a pdf >> >> pdf("MAplots.pdf") >> for(i in 1:8) plotMA(rg, array = i) >> dev.off() >> >> 3.) If on Windows (you don't mention OS) >> >> windows(record = TRUE) >> for(i in 1:8) plotMA(rg, array = i) >> >> Then use Page up and Page down keys to cycle through windows. >> >> HTH, >> >> Jim >> >> >> > >> > Regards, >> > Yanju >> >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Affymetrix and cDNA Microarray Core >> University of Michigan Cancer Center >> 1500 E. Medical Center Drive >> 7410 CCGC >> Ann Arbor MI 48109 >> 734-647-5623 >> >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues. >> >> _______________________________________________ >> 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 > > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.