[BioC] weights & normalizeBetweenArrays

[Gordon Smyth]

At 09:15 AM 1/02/2006, Jenny Drnevich wrote:
>Hello all,
>
>It appears that normalizeWithinArrays by default takes the weights 
>in an RGList into account when doing a normalization, but this does 
>not appear to be an option for normalizeBetweenArrays.

Yes.

>  I am correct that currently normalizeBetweenArrays will use all 
> the values equally for whichever norm method is chosen?

Yes.

>  If so, could this option be added in the future?

How and why this should be done isn't clear. Many of the between 
array methods do not have clear and obvious generalizations when 
there are quantitave weights, and there isn't so far any strong 
evidence that using the weights would produce a better result. Indeed 
using weights may be bad. For example, many people use weights to 
flag low intensity spots, and this is definitely not something which 
should be passed on to any of the between-array normalization 
methods. So we don't have any plans for it at this time.

Cheers
Gordon

>  I think I can hack the scale part of the code for my own purposes now...
>
>Thanks,
>Jenny
>
>
>Jenny Drnevich, Ph.D.
>
>Functional Genomics Bioinformatics Specialist
>W.M. Keck Center for Comparative and Functional Genomics
>Roy J. Carver Biotechnology Center
>University of Illinois, Urbana-Champaign
>
>330 ERML
>1201 W. Gregory Dr.
>Urbana, IL 61801
>USA
>
>ph: 217-244-7355
>fax: 217-265-5066
>e-mail: drnevich at uiuc.edu