[BioC] GCRMA explained in words

[Richard Friedman]

Dear Bioconductor list,

	I am trying to get a understanding
and verbal description of GCRMA.  I know that
it involves fitting for non-specific binding in
a GC-content dependent way, but it is not clear how.
If I were to explain RMA in words (thanks to Benilton and other
list members)  I would say that
the probe frequency vs intensity plot is fit with
a Guassian Model for noise and an exponential model
for signal. Is it correct to say that in GCRMA, the fit is
the same as in RMA but with set of probes of a given GC
content fit separately? If not, how would one put it with
comparable simplicity? I've read the papers several times
and some of the presentations on Dr. Irizarry's web-site,
and I am still not sure that I understand how the fit
is done.

Thanks and best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

"42 is the answer. Dylan got it wrong. 'Blowin'
in the wind' is not the answer. It isn't even
a number' " - Rose Friedman, age 9