[BioC] rma and MM

[Rafael A. Irizarry]

i want to add to ben's answer that the difference between the RMA
using MM for background and the current version is small. 

Some collegues and I are working on a new RMA that uses MM for
non-specific binding correction in such a way that it improves RMAs
accuracy a bit without lossing precision. By the end of june ill make this
work public. once you see the gains in accuracy you can decide if they are
worth the space.

On Tue, 24 Jun 2003, Ben Bolstad wrote:

> The current implementations of RMA do not use MM in any way (as you
> might calculate using rma() or expresso() or justRMA()). Some of the
> earlier versions used MM in the computation of the background, but this
> is no longer the case.
> 
> Thanks,
> 
> Ben
> 
> > We are having a little debate about whether RMA is using MM oligos at all.
> > I know that PM.only is the method that calls the gene expression index, but
> > Are MM intensities used in the calculation for the background correction?  I
> > thought I'd put this out to get the definitive answer.
> > 
> 
> -- 
> Ben Bolstad <bolstad at stat.berkeley.edu>
> http://www.stat.berkeley.edu/~bolstad
> 
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