On Fri, Apr 3, 2009 at 3:35 AM, Boyke Bunk <b.bunk@tu-braunschweig.de>wrote:

> Hello,
>
> we have got custom made Agilent microarrays read by a Genepix scanner.
> Every gene is spotted three times over the whole array.
>
> I preprocessed the arrays, how it is described by Yang and Paquet described
> in bioconductor testbook (using the marray library). Finally there is no
> summarization method mentioned, because in beta7 dataset every gene is
> obviously spotted once. Is there a common method available to summarize the
> three probes?
>

You might want to look at limma for analysis.  It allows one to deal with
replicate spots within a statistical framework when looking for
differentially-expressed genes.

Sean

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