[BioC] GCRMA explained in words

James W. MacDonald jmacdon at med.umich.edu
Wed Feb 8 14:34:48 CET 2006

Richard Friedman wrote:
> 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. 

This isn't an explanation of RMA, but an explanation of how the 
background is estimated when running RMA (an explanation of RMA would 
need to talk about robust model fitting).

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? 

Basically, yes. The idea is to 'bin' MM probes based on the GC content, 
and then estimate the background for each bin. Since the background 
binding will be affected by the GC content of the probes, you get a 
better estimate of background than you would if you ignore the GC 
content, which is what RMA does.

After background correction, GCRMA and RMA are identical.



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
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James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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