[BioC] Variance of M as a function of A in MA plots

[Andrew Harrison]

Hi,

	I've generated several MA/RI plots after using RMA and 
noticed that the standard deviation in M (fold change) is related 
to A (average intensity) - to derive the SD in M, only sample fold 
changes over a limited range in A (a similar calculation to the 
Quackenbush sliding Z-score). 

	When using RMA, the standard deviation in M is proportional 
to A, except for the largest intensities. However, when using 
expresso with all the options set to MAS, the standard deviation is 
independent of A. I believe the variance in M should be independent 
of A, in which case this suggests MAS is the way to go.

	Has anybody else seen this effect, or can suggest a remedy,  
or more likely a gap in my logic?

	Best wishes and thanks in advance,
		Harry

-- 
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Dr Andrew Harrison                               Tel: 44 (0) 207 679 3890   
Biomolecular Structure and Modelling Unit        Fax: 44 (0) 207 679 7193
Biochemistry and Molecular Biology Dept.     
University College London
Gower Street                       	   Email: harry at biochem.ucl.ac.uk
London, WC1E 6BT, UK                  http://www.biochem.ucl.ac.uk/~harry
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