[BioC] about plot rglist

[James W. MacDonald]

Hi Yanju,

Please don't send questions directly to me. Using the BioC list is 
preferred for at least two reasons. First, there are many people on the 
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yanju wrote:
> Dear James,
> 
> In analyse of DNA microarray using LIMMA, for example:
> targets<-readTargets("target.txt")
> rg<-read.maimages(targets$FileName,source="genepix",wt.fun=wtflags(0.1))
> 
> when I plot rg by using:
> plotMA(rg)
> Only one array has been plotted, but actually, I have 8 arrays . I tried 
> plotMA(rg, array=8), it did not work neither.
> I want to know how to plot MA imagin of multiple arrays.
> Expectin your reply. Thank you in advance.

As far as I know, plotMA() is only designed to plot one array at a time. 
If you want to plot all the arrays, you have several choices.

1.) Plot all together in one window

layout(matrix(1:8, nc = 2, byrow = TRUE))
for(i in 1:8) plotMA(rg, array = i)

2.) Make individual plots and save in a pdf

pdf("MAplots.pdf")
for(i in 1:8) plotMA(rg, array = i)
dev.off()

3.) If on Windows (you don't mention OS)

windows(record = TRUE)
for(i in 1:8) plotMA(rg, array = i)

Then use Page up and Page down keys to cycle through windows.

HTH,

Jim


> 
> Regards,
> Yanju


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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