Richard as Gordon pointed out, your needs may be satisfied by limma. To install arrayQualityMetrics, I think you first need to: - upgrade to a more recent version of R (at least 2.13.0) - install the system library libcurl, including C header files (You didn't provide sessionInfo() but it looks like you are running on Unix and use R 2.12) Best wishes Wolfgang Il Jun/25/11 9:52 AM, Richard ha scritto: > Wolfgang Huber<whuber at="" ...=""> writes: > >> >> Hi Richard >> >> Il Jun/19/11 4:19 AM, Richard Green ha scritto: >>> Could someone suggest the best way to create an MA plot from 14 single color >>> agilent arrays? I would really appreciate it. Thanks -Rich >>> >> >> One option is to compute a virtual mean (or median) reference array and >> to make 14 MA-plots of each array against that reference. Essentially, >> you redefine the 'A' to be the average of all arrays rather than just of >> a pair, and then compute 14 different 'M's. >> >> The MA plot is just an orthogonal transformation of the ordinary 2D >> scatterplot. In that sense, any other linear transformation of your >> 14-dimensional dataset could also be useful (e.g. PCA), in particular if >> one of the new axes aligns with the (1,1,1,..,1) direction. >> >> (A variant of the 'virtual reference array' idea is used in the MA plots >> in the reports generated by 'arrayQualityMetrics', which you can see by >> running the R script associated with the vignette >> http://www.bioconductor.org/packages/devel/bioc/html/arrayQualityMe trics.html >> -> "Introduction: microarray quality assessment with arrayQualityMetrics") >> >> Best wishes >> Wolfgang Huber >> EMBL >> http://www.embl.de/research/units/genome_biology/huber >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at ... >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > Hi Wolfgang, Thanks for your response. I tried to install arrayQualityMetrics > but was unable (see errors below). Not sure why, tried it on a couple of > different R installations. I did figure out how to create the individual MA > plots but am now just trying to figure out the simplest way to overlay two MA > plots on to each other to see how different they look. I have generated a PCA > but would like to compare pairs of arrays by MA plot. Any suggestion are > appreciated. I pasted my R script below: > source("http://www.bioconductor.org/biocLite.R") > library(limma) > setwd("/vol04/microarray/") > RG<- > read.maimages(files=dir(),source="agilent",columns=list(G="gMeanSign al",Gb="gBGM > edianSignal",R="gMeanSignal",Rb="gBGMedianSignal")) > RG<- backgroundCorrect(RG, method="normexp", offset=50) > RG<- normalizeBetweenArrays(RG$R, method="quantile") > RG<- log2(RG) > for (i in 1:24) { > fname<-paste("/vol04/microarray/ma_plot",i,".png",sep="") > png(fname,300,300) > print(plotMA(RG, array=i, cex=.2, ylim=c(-1.5,1.5))) > dev.off() > } > > The above works no problem but when I try to add more than one array I get > >> print(plotMA(RG, array=(1:3,13:16), cex=.2, ylim=c(-1.5,1.5))) > Error: unexpected ',' in "print(plotMA(RG, array=(1:3," >> print(plotMA(RG, array=1:13, cex=.2, ylim=c(-1.5,1.5))) > Error in xy.coords(x, y, xlabel, ylabel, log) : > 'x' and 'y' lengths differ > > > ###############quality metrics error ############################### > ERROR: configuration failed for package ?XML? > * removing ?/home/greener/R/x86_64-redhat-linux-gnu- library/2.12/XML? > ERROR: dependency ?XML? is not available for package ?SVGAnnotation? > * removing ?/home/greener/R/x86_64-redhat-linux-gnu- library/2.12/SVGAnnotation? > ERROR: dependencies ?SVGAnnotation?, ?XML? are not available for package > ?arrayQualityMetrics? > * removing ?/home/greener/R/x86_64-redhat-linux-gnu- > library/2.12/arrayQualityMetrics? > > _______________________________________________ > 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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber