Hi all, I have a couple of questions about unconnected experiments: - I understand that a pre-requisite for single channel analysis of two colour data is Aquantile normalization between arrays... but shall I normalize WITHIN arrays, too? - is there a way to export the normalized single-channel intensities from LIMMA? thank you, any help appreciated. Federico

> Date: Fri, 25 Feb 2005 17:34:18 -0800 > From: Federico Scossa <fscossa@pw.usda.gov> > Subject: [BioC] LIMMA - unconnected experiments > To: bioconductor@stat.math.ethz.ch > > Hi all, > I have a couple of questions about unconnected experiments: > > - I understand that a pre-requisite for single channel analysis of two > colour data is Aquantile normalization between arrays... but shall I > normalize WITHIN arrays, too? You need to do some sort of separate channel normalization, Aquantile is one possibility. Aquantile normalization between arrays is intended to be used in conjunction with loess normalization within arrays. Loess normlizes the M-values, Aquantile the A-values. Between them you have normalized the absolute intensities. > - is there a way to export the normalized single-channel intensities from > LIMMA? There are naturally many ways, but none are provided as built-in commands. Conversion is provided to exprSet objects. Other than that, I don't have any plans to implement export methods. Gordon > thank you, any help appreciated. > > Federico