[BioC] RMA - answer found

[Richard Friedman]

Naomi,

	I am trying to understand RMA better myself at the moment. I cannot 
understand how
the background is obtained from page 6 of the pdf file that you cite 
below. In
the RMA paper (Biostat 4, 249-264). Dr. Irizarry and coworkers state 
"An alternative
background correction is to consider B(PM(ijn))=E(sijn)|PMijn). ... To 
obtain a computationally
feasible B(.) we consider a closed form transformation obtained when 
sijn
is exponential and bgijn is normal."
	This text seems to refer to the graphs on page 6 of what you cite 
below, but I don't
understand it. Can you (or anybody out there) please explain it in 
simpler language.

Thanks and best wishes,
Rich

On Jan 30, 2006, at 5:24 PM, Naomi Altman wrote:

> I found the answer to my questions on Dr. Irizarry's website in his 
> talk:
>
> http://www.iobion.com/slides/RMA/rma.pdf
>
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111
>
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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.
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