Hi Rich, I am also interested in your Powerpoint slides. Could you send them to me or post them. Thanks, Shirley, On 2/20/07, Richard Friedman <friedman at="" cancercenter.columbia.edu=""> wrote: > 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 > > > > > > --------------------------------- > > We won't tell. Get more on shows you hate to love > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > ------------------------------------------------------------ > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >