[BioC] creating an MA plot with two single channel agilent arrays

[Richard Green]

Wow Gordon, thank you so much. This was extremely helpful. I was able to generate some new figures. I couldn't find a lot of info on mdplots() . I was able to generate a figure with my whole set of arrays but wasn't able to load two individual arrays into mdplots. 
My plan was to just have two overlaying MA plots from two different arrays in different colors. Any suggestions you have on the simplest way to achieve this I would be grateful. Again Thank you Gordon. I really appreciate it!
-Rich



On Jun 25, 2011, at 6:45 PM, Gordon K Smyth <smyth at wehi.EDU.AU> wrote:

> Hi Richard,
> 
> The function plotMA() only makes a single plot.  As the help page explains, the argument 'array' is an integer rather than a vector.  To see a number of plots side by side, you might try mfrow().  For example, to see 2 plots side by side:
> 
>   par(mfrow=c(1,2))
>   plotMA(x,array=1)
>   plotMA(x,array=2)
> 
> To see 4 plots:
> 
>   par(mfrow=c(2,2))
>   plotMA(x,array=1)
>   etc
> 
> If you have a set of 24 arrays, plotMA() will compare each individual array to the median-array constructed from all the arrays.
> 
> If you want to compare just two arrays, mdplot() is another convenient alternative.  It gives the same results as plotMA() with just two arrays.
> 
> Best wishes
> Gordon
> 
>> Date: Fri, 24 Jun 2011 16:01:02 -0700
>> From: Richard Green <greener at uw.edu>
>> To: bioconductor at r-project.org
>> Subject: [BioC] creating an MA plot with two single channel agilent
>>    arrays
>> 
>> 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
>> 
>> 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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