[BioC] Use of duplicateCorrelation

[Gordon K Smyth]

Dear Erika,

The output from fit() and eBayes() cannot be as you've given below, 
because eBayes() does not remove the $coefficient component of the fitted 
model object.  Can you please rerun your code from scratch in a new R 
session, re-reading the data and so on.

Best wishes
Gordon

> Date: Thu, 22 Jan 2009 15:51:43 +0100
> From: "Erika Melissari" <erika.melissari at bioclinica.unipi.it>
> Subject: [BioC] Use of duplicateCorrelation
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID: <00c001c97ca0$f1a27fe0$ba517283 at maanalysis>
> Content-Type: text/plain
>
> Hello all,
>
> I'm studing how to use duplicateCorrelation() of LIMMA package in order to evaluate the between-arrays correlation.
> I have a simple experiment of direct comparison with dye-swap as follows:
> targets
>  SlideNumber       FileName     Cy3     Cy5          Date
> 1                             Ag_1.gpr      wt1        1RP         20/9/2008
> 2                             Ag_2.gpr     1RP      wt1            20/9/2008
> 3                             Ag_3.gpr      wt2         2RP         8/11/2008
> 4                             Ag_4.gpr     2RP      wt2             8/11/2008
>
> I use duplicateCorrelation() as follows:
>
> design <- c(1,-1,1,-1)
>> biolrep<-c(1,1,2,2)
>> corfit<-duplicateCorrelation(MA,design,ndups=1,block=biolrep)
>> corfit$consensus
> [1] -0.5543286
>
> The correlation is negative because of dye-swap.
> Then, I evaluate linear model as explained in limma userguide:
>
>> fit<-lmFit(MA,design, block=biolrep,cor=corfit$consensus,weights=NULL)
>> summary(fit)
>                 Length Class      Mode
> coefficients     10807  -none-     numeric
> stdev.unscaled   10807  -none-     numeric
> sigma            10807  -none-     numeric
> df.residual      10807  -none-     numeric
> ndups                1  -none-     numeric
> spacing              1  -none-     numeric
> block                4  -none-     numeric
> correlation          1  -none-     numeric
> cov.coefficients     1  -none-     numeric
> pivot                1  -none-     numeric
> genes                5  data.frame list
> Amean            10807  -none-     numeric
> method               1  -none-     character
> design               4  -none-     numeric
> fit2<-ebayes(fit)
> summary(fit2)
>          Length Class  Mode
> df.prior      1  -none- numeric
> s2.prior      1  -none- numeric
> s2.post   10807  -none- numeric
> t         10807  -none- numeric
> p.value   10807  -none- numeric
> var.prior     1  -none- numeric
> lods      10807  -none- numeric
>> toptable(fit2,adjust="fdr")
> Error in dim(data) <- dim : attempt to set an attribute on NULL
>
>
>
> What does it means this error message and, above all, where is the mistake in my analysis procedure?
> I do not understand why in fit2 there are not any coefficients!
> I would like to evaluate the dye effect also. How can I do this?
> I tryed the inclusion of a dye effect coefficient in the design,
>
> design<-cbind(Dye=1,design)
>
> but when I calculate duplicateCorrelation corfit$consensus is NaN. Is it correct?
>
> Thanks very much for any kind of help in advance!
> Best regards
> Erika