[BioC] LIMMA: normalizeBetweenArrays
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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