[BioC] question about RefRMA (RefPlus)

[shirley zhang]

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
>