[BioC] How to normalize one additional CEL file?

[Richard Friedman]

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,
Rich


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
>       ------------------------------------------------------------
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> 
> 
> 
> 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
Lecturer
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Columbia University Medical Center
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