[BioC] LIMMA: normalizeBetweenArrays

Gordon Smyth smyth at wehi.edu.au
Tue Jul 27 00:35:36 CEST 2004

At 07:32 PM 26/07/2004, S_Thieme wrote:
>I've a question concerning Gquantile (also Rquantile) normalization 
>between arrays. Did I understand it right that this normalization 
>"prefers" one channel (G or R) without regarding the experimental design, 
>which may be given by a design matrix. So any dye swap is not respected.
>Is that right?

Yes. Gquantile normalization is designed for experiments with a common 
reference always on the green channel. Quantile normalization is applied to 
the green channels and then the red channel is adjusted proportionally for 
each spot on each array.

>For Tquantile: If I define targets for normalization all the other none 
>defined are not processed?

Tquantile applies quantile normalization separately to subgroups of 
channels. You should specify a target name for each channel on each array 
so that everything is normalized.

>  Or did they treated like using the composite normalization method ?

This has nothing to do with "composite" normalization, which is a 
within-array normalization technique.



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