[BioC] M vs A plots of affymetrix data

James W. MacDonald jmacdon at med.umich.edu
Thu Mar 9 15:57:05 CET 2006

michael watson (IAH-C) wrote:
> Hi
> I have seen many MvsA plots of affymetrix data (eg
> http://www.stat.berkeley.edu/users/terry/Classes/s246.2002/Week16/week16.pdf)
> and I want to recreate them for my own data.
> I realise that I have to take two arrays pairwise to get my ratio(M)
> and average(A), but does anyone know if these plots are generally at
> the probe level or at the gene level?
> If at the probe level, are they the ratio and average of just the PM
> intensities?
> Also, when I read data in using ReadAffy(), are the PM and MM
> intensities raw or on a logged scale?  If I then perform rma() or
> mas5(), are the gene level intensities on a log scale?  This is
> important, as I need to figure out how to calculate the ratio and
> average

Is there any reason not to use e.g., MAplot() or mva.pairs() in the affy 
package? These functions will do MA plots using the probe level data. If 
you want the expression values, there is always plotMA() in limma.

help(package = "thepackagename") is your friend.



> Many thanks Mick
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James W. MacDonald, M.S.
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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