I should add that the plotMA() function won't do this for all arrays automagically. However something like pdf("MAplots.pdf") lapply(1:ncol(matrixOfArrays), function(x) plotMA(matrixOfArrays, x)) dev.off() will do so. However, a pdf of 250 MA plots will be absolutely huge. Vector graphics with lots of points are not fun. Alternatives would be to create jpeg files, or to 'roll your own' using smoothScatter() instead of plot(). Something similar to maplot <- function(mat){ x <- apply(mat, 1, median, na.rm = TRUE) for(i in seq_len(ncol(mat))){ y <- mat[,i] - x smoothScatter(y~x, main = colnames(mat)[i], xlab = "A", ylab = "M") } } Best, Jim On 11/2/2011 10:43 AM, James W. MacDonald wrote: > Hi Juliet, > > On 11/2/2011 10:23 AM, Juliet Hannah wrote: >> All, >> >> I have illumina arrays (~250) and I was looking at the options for MA >> plots in the lumi package and the beadarray package. It seems they are >> all giving pairwise plots. >> >> When I have had a large number of Affy arrays, I have had success with >> the MAplot function in affyPLM because I believe it takes the median >> of all >> arrays and then gives me one pdf comparing each array to the reference. >> >> Does anyone know of a general function similar to this that I can use >> on a matrix. > > The plotMA() function in limma will do this. > > Best, > > Jim > > >> >> Thanks! >> >> Juliet >> >>> sessionInfo() >> R version 2.14.0 (2011-10-31) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] lumi_2.6.0 nleqslv_1.9.0 methylumi_2.0.0 Biobase_2.14.0 >> >> loaded via a namespace (and not attached): >> [1] affy_1.32.0 affyio_1.22.0 annotate_1.32.0 >> [4] AnnotationDbi_1.16.0 BiocInstaller_1.2.0 DBI_0.2-5 >> [7] grid_2.14.0 hdrcde_2.15 IRanges_1.12.0 >> [10] KernSmooth_2.23-6 lattice_0.20-0 MASS_7.3-16 >> [13] Matrix_1.0-1 mgcv_1.7-9 nlme_3.1-102 >> [16] preprocessCore_1.16.0 RSQLite_0.10.0 tools_2.14.0 >> [19] xtable_1.6-0 zlibbioc_1.0.0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

On 11/03/2011 04:15 AM, mjonczyk wrote: > Dear Juliet, > > you can also see plotMA3by2 function in limma, it produces pictures > (jpg, png, pdf) > with six arrays in each file. This command will print pictures for all > arrays. I find lattice to be useful in this context > library(lattice) > library(ALL) > data(ALL) > M = exprs(ALL) - exprs(ALL)[,1] > A = (exprs(ALL) + exprs(ALL)[,1]) / 2 > df = data.frame(M=as.vector(M[,-1]), A=as.vector(A[,-1]), + Id=sampleNames(ALL)[col(M[,-1])]) > xyplot(M~A|Id, df, layout=c(5,5), pch=".") Martin > > Best Wishes, > Maciej Jo?czyk > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793