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

[Susan Holmes]

Dear Andrew,
This is very often the case, I have found that Wolfgang Huber's
vsn package does a very good job of
taking out the variance's dependence on the intensity
especially in the lower ranges.
Best
Susan Holmes
Statistics



On Thu, 22 May 2003, Andrew Harrison wrote:

> 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
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 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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