Howdy,

I've been generating some individual MA plots but would now like to generate
an MA plot with two different arrays to compare them. Ideally I'd like the
two arrays to be different colors so
I can see how they differ
Pasted below is my R session. Any suggestions folks have is appreciated.
-Rich

source("http://www.bioconductor.org/biocLite.R")

library(limma)

setwd("/vol04/microarray/")

RG <-
read.maimages(files=dir(),source="agilent",columns=list(G="gMeanSignal",Gb="gBGMedianSignal",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
>

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