[BioC] about plot rglist

[James W. MacDonald]

This is a perfect example why it is better to send to the list instead 
of me ;-D

Jenny Drnevich wrote:
> 
> See ?plotMA3by2  - I use it quite often, because it makes MA plots of 
> all your arrays all on the same scale, puts 6 per page, and downloads 
> the resulting files into your working directory.
> 
> Cheers,
> Jenny
> 
> At 08:33 AM 9/12/2006, James W. MacDonald wrote:
> 
>> 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
>> BioC list who might have a better answer for your question. Second, the
>> list is archived and available for people to search, and your question
>> and any resulting answer may help someone in the future.
>>
>> 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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> 
> 
> Jenny Drnevich, Ph.D.
> 
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
> 
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
> 
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu


-- 
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


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.