[BioC] warning message from duplicateCorrelation in limma

[Na, Ren]

________________________________

From: Gordon K Smyth [mailto:smyth at wehi.EDU.AU]
Sent: Sat 5/14/2005 3:50 AM
To: Na, Ren
Cc: bioconductor at stat.math.ethz.ch
Subject: [BioC] warning message from duplicateCorrelation in limma



> 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.

Dr. Gordon Smith,

I thought "corfit<-duplicateCorrelation(MA,design,block=pair)" calculates the correlation between every slide and its dye swap ( a pair of technical replicates). I have 27 pairs of technical replicates here. Maybe I misunderstand the section " technical replicate" of User's guide. Please enlight me if I did anything wrong.  Then I can use lmFit and makeContrast to find out differential expression between any comparison I want to make.

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.

Yes, You are right. We had no biological replication in this experiment. This is a initial experiment. All RNA samples are extracted from cell culure dishs. The purpose of the experiment is try to find out differential expression between time points and that between genotypes, and locate which time point our interested genes changes. Then we focuse on that period time to do futher time point experiment.

Gordon




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