Hi all,

I have some troubles using the avereps function on Limma.

I process and analyse agilent one-color data without any problems but 
when I average replicate probes with avereps, the function create a good 
matrix but the new object is only a matrix containing the new 
intensities. Thus, I lose the Elist format with all associated 
informations (weights, probe name, gene name, etc...).
So my question is how to obtain a complete Elist (or RGlist or MAlist) 
object using this function.

Here is my script:

/library(limma)
targets=readTargets("target.txt", sep="\t")
Eraw=read.maimages(files=targets$FileName,source="agilent",names=targets$SampleName,channels=1)

E=new("EList")
E$E=Eraw$E
E$Eb=Eraw$Eb
E$weights=Eraw$weights
E$targets=Eraw$targets
E$genes=Eraw$genes
E$source=Eraw$source
E$printer=Eraw$printer

Enorm=E
Enorm$E=log2(normalizeBetweenArrays(Enorm$E,method="quantile"))

EnormAvRep=avereps(Enorm,ID=Enorm$genes$ProbeName)
/
It's here that the new object is a matrix containing only intensities 
values.

Thanks for your help.


-- 
Benoit Loup, PhD
UMR Biologie du Développement et Reproduction
Différenciation des Gonades et Perturbations
INRA -- Domaine de Vilvert
Bâtiment Jacques Poly
78350 Jouy en Josas
France

Tel: 33 1 34 65 25 38
Fax: 33 1 34 65 22 41
E-mail: benoit.loup@jouy.inra.fr


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