[BioC] M vs A plots of affymetrix data

[michael watson (IAH-C)]

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
 
Many thanks
Mick