[BioC] Single-Channel Normalization using Bioconductor

Wolfgang Huber huber at ebi.ac.uk
Wed Dec 7 15:01:35 CET 2005

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:

> 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?


> 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
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber

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