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? Thanks for your help Boyke -- Dipl.-Biol. Boyke Bunk Technische Universit?t Braunschweig Institute of Microbiology - Bioinformatics - Spielmannstr. 7 D-38106 Braunschweig Germany +49-(0)531-391 5810 b.bunk at tu-braunschweig.de

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 [[alternative HTML version deleted]]