> Date: Tue, 13 Jun 2006 10:22:08 +0200 > From: Christelle Dantec <christelle.dantec at="" igf.cnrs.fr=""> > Subject: [BioC] limma: duplicateCorrelation > To: bioconductor at stat.math.ethz.ch > Content-Type: text/plain > > Hi, > > I have a technical replicates with dye-swap as: > Cy3 Cy5 > ------------- > wt1 mu1 > mu1 wt1 > wt2 mu2 > mu2 wt2 > wt3 mu3 > mu3 wt3 > wt4 mu4 > mu4 wt4 > > > > designM <- c(1,-1,1,-1,1,-1,1,-1) > corfit<- duplicateCorrelation(MAlist, designM, bloc=c(1,1,2,2,3,3,4,4)) > fit<- lmFit(MAlist,design=designM,block=c(1,1,2,2,3,3,4,4), > correlation=corfit$consensus) > > but I have this error message: > Running plug-in: normalization.R > Warning in Too much damping - convergence tolerance not achievable > Error in paste(errMsg, "\n", sep = "") : argument "errMsg" is missing, > with no default > Execution halted > Failed to execute R-script > > This error appears when creating the corfit variable. > If someone can help me... > > Thanks > > Christelle Dear Christelle, It would appear from the error messsage that you are not using limma directly but rather are using a third-party "plug-in". The error message is occuring in the plug- in, not in the underlying limma functions. You should raise the problem with the author of the plug-in. Best wishes Gordon