[BioC] warning message from duplicateCorrelation in limma

[Na, Ren]

Hi,
I have a time course experiment in which three genptypes' RNAs (wt, mu1, mu2) are extracted at 5 time points. 
I used common reference design.

For time point 0, I have six arrays,
	cy3		cy5
array1	ref		wt_Notreatment
array2	wt_Notreatment	ref
array3	ref		mu1_Notreatment
array4	mu1_Notreatment	ref
array5	ref		mu2_Notreatment
array6	mu2_Notreatment	ref

For time point from 1 to 4, each time point has 12 arrays. six arrays are like above, samples are 
without treatment. And the other six arrays are for samples with treatment.

I did the following steps,

design<-modelMatrix(targets, ref="ref")
design<-cbind(Dye=1,design)
pair<-rep(1:27,each=2)
corfit<-duplicateCorrelation(MA,design,block=pair)
Warning message:
NaNs produced in: atanh(rho)
traceback()
No traceback available
corfit$consensus
[1] -1

what does Warning message mean here? and why corfit$consensus is -1? 
I used R version 2.0.0 and limma version 1.8.12, then I upgraded limma to version 1.9.0, and I got 
same Warning message from each version of limma.
Any help will be greatly appreciated.
Thanks!!

Ren




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