[BioC] Re: rma background correction

[Rafael A. Irizarry]

you can read the reference below for some details or look at the code
for all the details: "bg.correct.rma"

http://stat-www.berkeley.edu/users/bolstad/stuff/BAUGM.pdf has a bit 
more than the reference.

a quick summary: it uses the PM distribution to get an overall 
background level. then a transformation based, on a 
background nosie + signal model is used.

Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, 
Antonellis, KJ, Scherf, U, Speed, TP (2003)  Exploration, Normalization, 
and Summaries of High Density Oligonucleotide Array Probe Level Data. 
Biostatistics. Vol. 4, Number 2: 249-264.


On Wed, 25 Jun 2003 
johnston at pat.biochem.ucl.ac.uk wrote:

> Hi,
> 
> Regarding the discussion of the rma background correction: If it doesn't use 
> the MM values to estimate bg anymore, what is the background correction 'rma' 
> in expresso actually doing?
> 
> Many Thanks,
> 
> Cass. 
> 
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