Dear Erika, The output from fit() and eBayes() cannot be as you've given below, because eBayes() does not remove the $coefficient component of the fitted model object. Can you please rerun your code from scratch in a new R session, re-reading the data and so on. Best wishes Gordon > Date: Thu, 22 Jan 2009 15:51:43 +0100 > From: "Erika Melissari" <erika.melissari at="" bioclinica.unipi.it=""> > Subject: [BioC] Use of duplicateCorrelation > To: <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <00c001c97ca0$f1a27fe0$ba517283 at maanalysis> > Content-Type: text/plain > > Hello all, > > I'm studing how to use duplicateCorrelation() of LIMMA package in order to evaluate the between-arrays correlation. > I have a simple experiment of direct comparison with dye-swap as follows: > targets > SlideNumber FileName Cy3 Cy5 Date > 1 Ag_1.gpr wt1 1RP 20/9/2008 > 2 Ag_2.gpr 1RP wt1 20/9/2008 > 3 Ag_3.gpr wt2 2RP 8/11/2008 > 4 Ag_4.gpr 2RP wt2 8/11/2008 > > I use duplicateCorrelation() as follows: > > design <- c(1,-1,1,-1) >> biolrep<-c(1,1,2,2) >> corfit<-duplicateCorrelation(MA,design,ndups=1,block=biolrep) >> corfit$consensus > [1] -0.5543286 > > The correlation is negative because of dye-swap. > Then, I evaluate linear model as explained in limma userguide: > >> fit<-lmFit(MA,design, block=biolrep,cor=corfit$consensus,weights=NULL) >> summary(fit) > Length Class Mode > coefficients 10807 -none- numeric > stdev.unscaled 10807 -none- numeric > sigma 10807 -none- numeric > df.residual 10807 -none- numeric > ndups 1 -none- numeric > spacing 1 -none- numeric > block 4 -none- numeric > correlation 1 -none- numeric > cov.coefficients 1 -none- numeric > pivot 1 -none- numeric > genes 5 data.frame list > Amean 10807 -none- numeric > method 1 -none- character > design 4 -none- numeric > fit2<-ebayes(fit) > summary(fit2) > Length Class Mode > df.prior 1 -none- numeric > s2.prior 1 -none- numeric > s2.post 10807 -none- numeric > t 10807 -none- numeric > p.value 10807 -none- numeric > var.prior 1 -none- numeric > lods 10807 -none- numeric >> toptable(fit2,adjust="fdr") > Error in dim(data) <- dim : attempt to set an attribute on NULL > > > > What does it means this error message and, above all, where is the mistake in my analysis procedure? > I do not understand why in fit2 there are not any coefficients! > I would like to evaluate the dye effect also. How can I do this? > I tryed the inclusion of a dye effect coefficient in the design, > > design<-cbind(Dye=1,design) > > but when I calculate duplicateCorrelation corfit$consensus is NaN. Is it correct? > > Thanks very much for any kind of help in advance! > Best regards > Erika