[BioC] avereps problem

[Gordon K Smyth]

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 at jouy.inra.fr>
> To: Bioconductor mailing list <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] avereps problem
> Message-ID: <4CC547A0.3090903 at 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 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 at jouy.inra.fr