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