[BioC] warning message from duplicateCorrelation in limma

[Gordon K Smyth]

> Date: Thu, 12 May 2005 14:39:48 -0500
> From: "Na, Ren" <Na at uthscsa.edu>
> Subject: [BioC] warning message from duplicateCorrelation in limma
> To: <bioconductor at stat.math.ethz.ch>
>
> 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

>From your description of your experiment you seem to have confounded blocks entirely with
treatment effects, and it just isn't possible to sensibly estimate a within-block correlation in
this situation.  I'm actually a bit disappointed that duplicateCorrelation() gives you have value
here for $consensus: I would prefer it gave you NA, which it did when I tried to reproduce your
result.

Why are you setting 'block=pair'?  This seems to imply that you have no biological replication for
any of your treatments, which would be a very serious design flaw for your experiment.

Gordon