[BioC] M vs A plots of affymetrix data

[michael watson (IAH-C)]

Hi Jim
 
The MAplot() help is a little sparse, so I was trying to figure out how to do it from first principles, however I have subsequently found the http://bioinf.wehi.edu.au/marray/jsm2005/lab3/lab3.html lab which gives details on a few more of the arguments.
 
I've just seen Ben's e-mail too, which answers my next question which was going to be about plotting MvsA plots for the normalised data :)
 
Many thanks
Mick

________________________________

From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
Sent: Thu 09/03/2006 2:57 PM
To: michael watson (IAH-C)
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] M vs A plots of affymetrix data



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.

Best,

Jim


>
> Many thanks Mick
>
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
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