[BioC] Quantile normalization without using affyBatch

James W. MacDonald jmacdon at med.umich.edu
Tue Apr 19 19:26:29 CEST 2005

Shinhan Shiu wrote:
> 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.

How about normalizeBetweenArrays() in the limma package?


> Shinhan
> ********************************
>  Shinhan Shiu
>  Dept. of Ecology and Evolution
>  University of Chicago
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James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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