[BioC] Quantile normalization without using affyBatch

[Shinhan Shiu]

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


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  Shinhan Shiu
  Dept. of Ecology and Evolution
  University of Chicago