[BioC] Treatment of Duplicate spots

[Pita]

I have 3 questions:

How are duplicate spots treated when performing the 
normalizationWithinArrays? Are they treated separately as far as the 
regression is concerned?

How are duplicate spots treated when performing the 
normalizationBetweenArrays? Are they somehow treated together in the scale 
normalization or independently? For the case of using quantile 
normalization, is the number of quantiles the total number of spots on the 
chip, or it is for the case of duplicate spotting, the number of quantiles 
are n-spots/2, where each pair are adjusted together in some way?

For the case of duplicate spotting, what is the significance of merging the 
raw channels seperately prior to creating MA values with the loess 
normalization, then between chip scaling.

How many spots in a chip would be required to run quantile normalization vs 
scale normalization when using normalizeBetweenArrays?

Thanks for any insight into this. I am not a statistician, so I am 
unfamiliar with the ramifications of duplicate treatment in regression and 
in normalization.

Peter W.



At 12:16 PM 2/7/2005, Rhonda DeCook wrote:
>Recent posts have made me aware of the 'geneplotter' package.  This is 
>exactly
>what I've been wanting to do, but for the ath1121501 chip (Arabidopsis) which
>does not have an annotation package available at the metadata page yet.
>
>Past posts suggest folks are working on getting the annotation for this chip
>built...
>https://stat.ethz.ch/pipermail/bioconductor/2004-August/005818.html
>
>I was just wondering if anyone had new information on the progress of 
>building
>this annotation package.
>
>
>Rhonda
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor