Dear Gordon,
Thank you for your help. This exactly what I need I think.
May I ask you some more help ? I would like to know whether the script 
below is correct :

There are 4 biological experiments : F, H, O and CB
and there is 1 treatment with three levels: T , C and CL

I'd like to know genes that are differentially expressed between "C" and 
"T", and between "CL" and "C":

 > #
 > # Normalized data are in Dnorm
 > exp<-c("F","F","F","H","H","H","H","O","O","O","CB","CB","CB","CB")
 > corfit<-duplicateCorrelation(Dnorm, block=exp)
 > corfit$consensus
[1] -0.07705255
 > tr<-c("T","C","CL","T","C","CL","T","C","CL","T","C","CL")
 > tr<-factor(tr, levels=c("T","C","CL"))
 > design<-model.matrix(~tr)
 > fit<-lmFit(Dnorm,design, block=exp, cor=corfit$consensus)
 > fit<-eBayes(fit)
 > # comparison between treatment C and T
 > ttC<-topTable(fit, coef="trC", p.value=0.01, n=Inf)
 > dim(ttC2)
[1] 8834    7
 > # comparison between treatment CL and C
 > cont.matrix<-cbind("CLvsC"=c(0,1,-1))
 > fitCCL<-contrasts.fit(fit2, cont.matrix)
 > fitCCL<-eBayes(fitCCL)
 > ttCCL<-topTable(fitCCL, coef=1, p.value=0.01, n="Inf")
 > dim(ttCCL)
[1] 8798    7
 >

Thank you for your help
Christian

Gordon K Smyth a écrit :
> Dear Christian,
>
> See Section 8.2 of the limma User's Guide.  The 'block' argument of 
> duplicateCorrelation() and lmFit() handles random effects.
>
> Best wishes
> Gordon
>
>> Date: Fri, 25 Sep 2009 08:33:43 +0200
>> From: Christian Bri?re <briere@scsv.ups-tlse.fr>
>> Subject: [BioC] mixed models analysis with limma
>> To: bioconductor@stat.math.ethz.ch
>> Content-Type: text/plain
>>
>> Hello,
>>
>> I would like to know whether it is possible to analyze microarray data
>> from a mixed model experiment with Limma package.
>> I have 4 independent experiments (random effect) and 3 treatments (fixed
>> effect), and 1 microarray (monocolor) for each combination of the two
>> factors.
>>
>> Thank you for your help
>> -- 
>>
>> Christian Bri?re
>> UMR CNRS-UPS 5546
>> BP42617 Auzeville
>> F-31326 Castanet-Tolosan (France)
>> tel: +33(0)5 62 19 35 90
>> Fax: +33(0)5 62 19 35 02
>> E-mail: briere@scsv.ups-tlse.fr <mailto:briere@scsv.ups-tlse.fr>
>>
>> http://www.scsv.ups-tlse.fr
>> http://www.gdr2688.ups-tlse.fr 
>> <http://www.gdr2688.ups-tlse.fr/index.php>
>> http://www.ifr40.cnrs.fr


-- 

Christian Brière
UMR CNRS-UPS 5546
BP42617 Auzeville
F-31326 Castanet-Tolosan (France)
tel: +33(0)5 62 19 35 90
Fax: +33(0)5 62 19 35 02
E-mail: briere@scsv.ups-tlse.fr <mailto:briere@scsv.ups-tlse.fr>

http://www.scsv.ups-tlse.fr
http://www.gdr2688.ups-tlse.fr <http://www.gdr2688.ups-tlse.fr/index.php>
http://www.ifr40.cnrs.fr

 


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