>Date: Tue, 6 Dec 2005 12:34:19 -0800 >From: "Paul Lang" <paul.lang at="" oregonstate.edu=""> >Subject: [BioC] Single-Channel Normalization using Bioconductor >To: <bioconductor at="" stat.math.ethz.ch=""> > > > >Hello All, > >I am looking for a function or package in R / Bioconductor that can >normalize single-colour cDNA arrays. > >The experimental design contains three biological replicate chips for five >time points (control and four points after treatment) and four treatment >groups (strains of a given animal). > >The chip contains spiked-in controls at 5 orders of magnitude, and also >housekeeping genes. > >I've used vsn but it didn't seem to change the shape of the clouds. > >Any pointers or advice would be appreciated - let me know if you need more >details. > >With kind thanks in advance, > >Paul Lang >Oregon State University Other choices are normalize.quantiles() in the affy package or normalizeBetweenArrays() in the limma package. Apart from vsn, the choices are quantile normalization or simple scale normalization. Gordon