You have to specify the design matrix to duplicateCorrelation(). Gordon On Mon, 28 Sep 2009, Christian Bri?re wrote: > 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 ?crit : >> 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 at="" scsv.ups-tlse.fr=""> >>> Subject: [BioC] mixed models analysis with limma >>> To: bioconductor at 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 at scsv.ups-tlse.fr <mailto:briere at="" 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 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 at scsv.ups-tlse.fr <mailto:briere at="" 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 > > > >