Question: Use of duplicateCorrelation

0

Erika Melissari •

**240**wrote: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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