[BioC] RMA - answer found

[Ben Bolstad]

I'm not sure I want to take the risk of addressing it in "simpler
language" but a derivation of the correction formula is given on pages
17-21 of this document

http://bmbolstad.com/Dissertation/Bolstad_2004_Dissertation.pdf


On Mon, 2006-01-30 at 18:13 -0500, Richard Friedman wrote:
> 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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
> ------------------------------------------------------------
> 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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor