[BioC] One-color spotted microarrays analysis

Mark Cowley m.cowley0 at gmail.com
Fri May 22 03:05:41 CEST 2009

Hi Pier-Luc,
What sort of within array normalisation are you trying to perform? ie  
what issues have you spotted in your data that you think need removing?

There are no print-tip's as such on an agilent array since they're  
printed by fancy ink jet printers.
You can't do lowess, unless you make a 'virtual' 2nd channel, perhaps  
by taking the average of all channels.

Mark Cowley, PhD

Peter Wills Bioinformatics Centre
Garvan Institute of Medical Research, Sydney, Australia
On 22/05/2009, at 12:47 AM, Pier-Luc Poulin wrote:

> Hi Massimo and everyone,
> Thanks for the suggestion. I've read documentation about  
> Agi4x44PreProcess
> and Affy packages but I still need advice. Agi4x44PreProcess  
> contains no
> method for normalization between print tips within arrays.
> Our data consists of single color spotted chips. We need to find a way
> in bioconductor to do within array normalization. Limma's  
> normalizeWithinArrays
> and marray's maNormMain only do that for two color arrays. I haven't  
> find
> any function for normalizing single channel arrays, except for  
> affymetrix chips.
> Thanks
> P-L Poulin
> Research assistant
> Université Laval
> www.arborea.ca
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