[BioC] how to use normalizeForPrintorder accounting for duplicates when there are spots that are not duplicated in the array?

[Gordon K Smyth]

Dear Artur,

You question doesn't really make sense, because print-order normalization has nothing to do with
duplicated spots.  The identities of the probes are ignored in such a normalization.  In any case,
you can't move spots around and expect the function to still keep track correctly of the print
order.  In the limma package, handling of duplicated spots is done post-normalization.

Best wishes
Gordeon

> Date: Wed, 20 Jun 2007 15:40:18 -0400
> From: "Artur Veloso" <abveloso at gmail.com>
> Subject: [BioC] how to use normalizeForPrintorder accounting for
> 	duplicates	when there are spots that are not duplicated in the array?
> To: "Bioconductor List" <bioconductor at stat.math.ethz.ch>
>
> Hi all,
>
> I am very new to microarray analysis and I'm running into a few issues with
> normalizations for the print order. The arrays I am working with are
> "home-made" and the spots are duplicated and separated by columns.
>
> My problem arises from the fact that there are non-informative spots (i.e.
> landing lights and empty spots) that are not duplicated. Would it be
> acceptable for me to take all these uninformative spots and shift them to
> the end of my spots list so that they didn't interfere with the informative
> and properly duplicated spots? Could this interfere with the results that
> I'd get from the function normalizeForPrintorder?
> If shifting the position of my spots like that isn't a good idea, does
> anyone have a suggestion to me?
>
> Thank you all very much,
>
> Artur Veloso