[BioC] Quantile normalization without using affyBatch

[Ben Bolstad]

> 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.

normalize.quantiles() operates directly on a matrix by quantile
normalizing columns.