Dear Gordon,

thank you very much for your reply. I think my mistake in those regards was
caused by the fact that the function printorder allows one to specify the
number of duplicates in the array.

In an unrelated issue, I've been using limma to analyze single channel cDNA
arrays and many times ran into errors message like "List must contain
components R and G" generated by the lack of the second channel on my
arrays. My solution was to change the code for almost all the functions that
I used on the pre-processing stage. Basically, I just removed the parts of
the code that referred to the non-existing channel.
I just wanted to bring awareness to this issue and offer to e-mail you the
changes I made on the functions to make them more suitable for my situation.

All the best,

Artur Veloso

On 6/21/07, Gordon K Smyth <smyth@wehi.edu.au> wrote:
>
> 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@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@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
>
>
>

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