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Question: how to make an MA plot with single color agilent microarray?
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gravatar for Richard Green
5.9 years ago by
Richard Green90 wrote:
Could someone suggest the best way to create an MA plot from 14 single color agilent arrays? I would really appreciate it. Thanks -Rich [[alternative HTML version deleted]]
ADD COMMENTlink modified 5.8 years ago by Gordon Smyth30k • written 5.9 years ago by Richard Green90
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gravatar for Wolfgang Huber
5.9 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
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/arrayQualityMetri cs.html -> "Introduction: microarray quality assessment with arrayQualityMetrics") Best wishes Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD COMMENTlink written 5.9 years ago by Wolfgang Huber13k
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gravatar for Gordon Smyth
5.8 years ago by
Gordon Smyth30k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth30k wrote:
Dear Richard and Wolfgang, The strategy of plotting relative to a reference array that Wolfgang mentions, is what limma does automatically for single channel data. Best wishes Gordon > Date: Sat, 25 Jun 2011 07:52:20 +0000 > From: Richard <greener at="" uw.edu=""> > To: <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] how to make an MA plot with single color agilent > microarray? > > 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? ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD COMMENTlink written 5.8 years ago by Gordon Smyth30k
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