Thank you Gordon,

Effectively I don't have the last version of limma:

/ sessionInfo()
R version 2.9.1 (2009-06-26)
i386-pc-mingw32

locale:
LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] limma_2.18.2
/
I will try to upgrade my version of limma.
Otherwise, I found a method to solve my problem creating a MAlist to 
which I apply the avereps function and then re-create an Elist.

/Ema=new("MAList", list(targets=Ebgnorm.median$targets, 
weights=Ebgnorm.median$weights, printer=Ebgnorm.median$printer, 
genes=Ebgnorm.median$genes, source=Ebgnorm.median$source, M=Ebg$Eb, 
A=Ebgnorm.median$E))
E.avg <- avereps(Ema, ID=Ema$genes$ProbeName)
Ebgnorm.median2=new("EList", list(targets=E.avg$targets, 
weights=E.avg$weights, printer=E.avg$printer, genes=E.avg$genes, 
source=E.avg$source, E=E.avg$A))/

Thanks a lot.

Best regards,

Benoit

Le 27/10/2010 00:06, Gordon K Smyth a écrit :
> Dear Benoit,
>
> The EList method for avereps() was introduced in limma 3.3.16 on 2 
> April 2010.  Your version of limma is probably older.  Type
>
>   sessionInfo()
>
> Best wishes
> Gorodn
>
>> Date: Mon, 25 Oct 2010 11:02:24 +0200
>> From: Benoit Loup <benoit.loup@jouy.inra.fr>
>> To: Bioconductor mailing list <bioconductor@stat.math.ethz.ch>
>> Subject: [BioC] avereps problem
>> Message-ID: <4CC547A0.3090903@jouy.inra.fr>
>> Content-Type: text/plain
>>
>> 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 D?veloppement et Reproduction
>> Diff?renciation des Gonades et Perturbations
>> INRA -- Domaine de Vilvert
>> B?timent 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

-- 
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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