[BioC] Normalization of expression values

[Steve Lianoglou]

Hi,

On Tue, Jul 27, 2010 at 7:19 PM, dorothyc <dorothyc at bcgsc.ca> wrote:
> Hi,
>
> I'm trying to normalize a table of probe level intensities (pls. see attachment).  Would you recommend a method, which would take only a matrix but not an AffyBatch or object and do quantile normalization, in R/Bioconductor packages.
>
> I came across normalize.quantiles {affy} but got the following errors:
> ------
>> library(affy)
>> normalize.quantiles(intensity.M,copy=TRUE)
> Error: could not find function "normalize.quantiles"
> ------

How about:

R> library(limma)
R> normalizeBetweenArrays(intensity.M, method='quantile')

>
> Thanks,
> Dorothy
>
>
>
>
>
>
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact