[BioC] question about RefRMA (RefPlus)

[Richard Friedman]

Jim,

	I am not acquainted with RefRMA but I have prepared Powerpoint slides 
explaining
RMA and GCRMA at what I believe is an introductory level (it was also 
my way of explaining
it to myself). I can send these to you under separate cover if these 
might help, or post them
if there is general interest and if it is allowed.

Best wishes,
Rich

On Feb 19, 2007, at 8:05 PM, James Anderson wrote:

>   Hi,
>     I think the rough idea of RefRMA is to use the training set cel 
> images to do RMA normalization, then we have a model how to map every 
> cel image to an intensity vector for training sample. For the cel 
> image file for test samples, apply the same mapping to get the 
> intensity for each test sample, based on the model obtained by RMA 
> normalization with training samples ONLY. My questions are:
>
>    Could      anybody explain to me EXACTLY what RMA does? I know 
> roughly what RMA does,      but not clearly about the process of 
> converting cel image file to an      intensity vector for each sample
>    Suppose      my case is I have two sites (say, they are both affy 
> files, each site has      50 samples), I want to train the samples 
> measured at site 1 to classify      the samples in site 2. Suppose 
> there are some obvious systematic      difference between the two 
> sites, for example, site 1 is measured with      much brighter light 
> than sight 2, so that the image of site 2 files are      always dimmer 
> than site 1. Does RefRMA (or RefPlus) account for this (systematic 
> bias) when      normalizing each sample in test site 2 to test site 1?
>
>   Thank you very much!
>
>   James
>
>
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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/

"My story 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