Deal All, I would like to know if there is in BioC a normalization method suitable for arrays where RNA samples are hybridazed with genomic DNA as common reference. the channel with the gDNA would be always constant and strong for every spot and of course we cannot apply any method that assumes an average equal expression level for both channels... what do you reckon? thank you very much in advance. Best regards. Emanuele

Hi Emanuele, first a naughty question: why did you choose this experimental design (gDNA as a reference) if you didn't have a plan for how to proceed with the data? One thing you could try is to simply forget about the reference and essentially treat the arrays as if they were single-color. There are a number of single-color normalization methods, including vsn (package vsn) and quantiles normalization (package affy). You could still use the reference channel for spot QC. But I would also be interested to see if anyone had an idea for how to more gainfully employ the reference channel. Ciao. Wolfgang marchiem@libero.it wrote: > Deal All, > I would like to know if there is in BioC a normalization method suitable for arrays where RNA samples are hybridazed with genomic DNA as common reference. > the channel with the gDNA would be always constant and strong for every spot and of course we cannot apply any method that assumes an average equal expression level for both channels... > what do you reckon? > thank you very much in advance. > > Best regards. > > Emanuele > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber