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
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