[BioC] Quantile normalization without using affyBatch

Suresh Gopalan gopalans at comcast.net
Tue Apr 19 20:07:44 CEST 2005

normalize.quantiles(matrixofvalues) should work.


(Suresh Gopalan, PhD)
----- Original Message ----- 
From: "Shinhan Shiu" <shiu at uchicago.edu>
To: <bioconductor at stat.math.ethz.ch>
Sent: Tuesday, April 19, 2005 12:52 PM
Subject: [BioC] Quantile normalization without using affyBatch

>I am working on Arabidopsis tiling array data. I want to adjust the 
>intensity based on GC content then do normalization. But the CDF and CEL 
>files are not available so the sequences and raw intensities are downloaded 
>from Gene Expression Omnibus instead.
> I have extracted codes from gcrma and the hacked version works fine for 
> background correction and affinity adjustment. I run into trouble, 
> however, when I try to do quantile normalization.
> The method "normalize" takes an affyBatch object but I am working with a 
> matrix of numbers. I wonder if there is any work around or other methods I 
> can use.
> Shinhan
> ********************************
>  Shinhan Shiu
>  Dept. of Ecology and Evolution
>  University of Chicago
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> Bioconductor at stat.math.ethz.ch
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