[BioC] GCRMA explained in words

[Richard Friedman]

Jim,

	Thanks!. So I do understand GCRMA! I should have said the "background 
correction portion"
of GCRMA which is the part I was having trouble with. I realize that 
the background correction
portion is followed quantile normalization and robust multichip 
summarization via (according to my
most recent information) median polish.


Best wishes,
Rich

On Feb 8, 2006, at 8:34 AM, James W. MacDonald wrote:

> 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.
>
> HTH,
>
> Jim
>
>
> 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
> 734-647-5623
>
------------------------------------------------------------
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