[BioC] GCRMA Bayes theory question

[Richard Friedman]

Anne,

	People were kind enough to help me with basically the same question,
so that I will hazard a summary and let more knowledgeable people add 
or correct
if necessary,

	In RMA the of the frequency of the intensity of individual probes are 
plotted against
intensity. It is assumed that the noise varies as a Gaussian function 
and that the signal
varies as an exponential. The plot is fit to a Gaussian which is 
subtracted out, leaving
only the signal. In GCRMA this is done separately for each set of 
probes with a given GC content.
Then the distribution of probes on different chips are normalized to 
give (almost) the same distribution
using quantile normalization. Finally the intensity of a probeset is 
obtained from its component
probes by fitting to a linear model using a robust method called medium 
polish.

	I hope this makes sense.
	There are people out there who can correct me if necessary.

Best wishes,
Rich

On Aug 24, 2006, at 3:19 AM, Anne Pohrt wrote:

> Hi,
>
> I am trying to understand how exactly the gcrma software works, and 
> working my way through the Wu/Irizarry paper "A Model Based Background 
>  Adjustment for Oligonucleotide Expression Arrays" .
> My problem is in understanding the Bayes approach that is behind it. I 
> am particularly interested in how the integrated functions look like.
> Could anyone point me towards a source of the functions or a source 
> with more detail than the paper I mentioned above?
>
> Any help would be very much appreciated,
> Best regards,
> Anne Pohrt
>
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------------------------------------------------------------
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.
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(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

"My novel has a hundred characters and it takes place over a year.
When I finish it, if it is shorter than Ulysses, then Joyce described 
things
too much".
-Rose Friedman, age 9