[BioC] how to make an MA plot with single color agilent microarray?

[Richard]

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/arrayQualityMetrics.html 
>   -> "Introduction: microarray quality assessment with arrayQualityMetrics")
> 
> Best wishes
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
> 
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> 
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="gMeanSignal",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 âXMLâ
* removing â/home/greener/R/x86_64-redhat-linux-gnu-library/2.12/XMLâ
ERROR: dependency âXMLâ is not available for package âSVGAnnotationâ
* removing â/home/greener/R/x86_64-redhat-linux-gnu-library/2.12/SVGAnnotationâ
ERROR: dependencies âSVGAnnotationâ, âXMLâ are not available for package 
âarrayQualityMetricsâ
* removing â/home/greener/R/x86_64-redhat-linux-gnu-
library/2.12/arrayQualityMetricsâ