[BioC] How to normalize one additional CEL file?

Richard Friedman friedman at cancercenter.columbia.edu
Tue Aug 17 20:50:24 CEST 2010

Dear Wiktor,

 	I was imprecise. fRMA, unlike RMA, gives the same normalization
for each sample independt of the other samples. I have not as yet used
it myself. Also, I am not familiar with affy miRNA chips or if there is
an fRMA funcion for them yet.

I hope this helps,

On Tue, 17 Aug 2010, Wiktor Mazin wrote:

> Dear Rich (and Vincent),
> Thanks for making me aware of the fRMA package that does look interesting.
> However, why do I have to normalize all of the cels with fRMA at the beginning?
> In my case, the new samples will arrive sequentially and it will not be possible to normalize all cels at once. Is fRMA then still a good option?
> Also, I'm looking into miRNA samples - but I guess this is no problem as long as I use the function makeVectorPackage in frmaTools, right?
> Thanks for your assistance.
> best gards,
> Wiktor
> On Fri, Aug 13, 2010 at 6:24 PM, Richard Friedman <friedman at cancercenter.columbia.edu> wrote:
>       Dear Wiktor,
>              I believe that the fRMA package will enable you to do what you want.
>       You would have to normalize all of the cels with fRMA athe the beginning.
>       Best wishes,
>       Rich
>       ------------------------------------------------------------
>       Richard A. Friedman, PhD
>       Associate Research Scientist,
>       Biomedical Informatics Shared Resource
>       Herbert Irving Comprehensive Cancer Center (HICCC)
>       Lecturer,
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>       In Memoriam,
>       George Scithers
> On Aug 12, 2010, at 8:28 AM, Wiktor Mazin wrote:
>       Dear List,
>       Suppose you normalize a training set in some way (RMA, etc.) to create a
>       predictor and then you want to apply this predictor on a single-CEL-file basis,
>       that is, your test set consists of only 1 new CEL file. (actually your test set
>       may consist of several new CEL files but they have to preprocessed and predicted
>       individually)
>       How can you preprocess / normalize one (test set) CEL file with the same
>       settings used to preprocess the training set? (NB! training and test set may not
>       be normalized together!)
>       Are there some functions / packages that allow this, or would you suggest
>       another way of dealing with this?
>       Looking forward to hearing from you.
>       Best regards,
>       Wiktor Mazin
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Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Biomedical Informatics Shared Resource
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

"The last 250 pages of the last Harry Potter
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happened in that day. All of Ulysses takes
place in one day and nothing happened in that day."
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