[BioC] Single-Channel Normalization using Bioconductor

Gordon Smyth smyth at wehi.edu.au
Thu Dec 8 02:06:49 CET 2005

>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 
>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.


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