[BioC] limma: duplicateCorrelation

[Gordon K Smyth]

> 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