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@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,
> Department of Biomedical Informatics (DBMI)
> Educational Coordinator,
> Center for Computational Biology and Bioinformatics (C2B2)/
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> Room 824
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> 1130 St. Nicholas Ave
> New York, NY 10032
> (212)851-4765 (voice)
> friedman@cancercenter.columbia.edu
> http://cancercenter.columbia.edu/~friedman/<http://cancercenter.columbia.edu/%7Efriedman/>
>
> 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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>>
>
>

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