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Hi Paul, Paul Lang wrote: > > Hello All, > > I am looking for a function or package in R / Bioconductor that can normalize single-colour cDNA arrays. There are quite a lot of these, basically everything that works with Affymetrix genechips data does it. See the chapter on Affymetrix preprocessing in the book: http://www.amazon.com/gp/product/0387251464 > > 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. What is it that are you trying to achieve and how is that related to changing the shape of the clouds? Can you post scatterplots or similar of your data before and after normalization or be more specific about what you think goes wrong? Cheers Wolfgang > 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 ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber