[BioC] Single-Channel Normalization using Bioconductor

[Gordon Smyth]

>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