[BioC] M vs. A plot

James W. MacDonald jmacdon at med.umich.edu
Tue Nov 23 18:44:59 CET 2004

kvyas wrote:
> Hi all,
> I am trying to make a M vs. A plot of an array. I don't know how to get my 
> data in the correct format for the MAplot command in affy. How do I get my 
> data in the correct format after Data <- ReadAffy()? Any help is appreciated.

Your data *is* in the correct format at this point. You should be able 
to simply do


to get the MA plot(s). Note that this function plots each chip versus a 
pseudo-median chip, so it may not be what you are expecting. If you want 
MA plots for all possible comparisons, you should use the mva.pairs() 
function. Note that this function expects a matrix of data, so you will 
have to first extract the PM or MM data using the pm() accessor function.




> Thanks!
> Kanan
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James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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