[BioC] Use of duplicateCorrelation
Gordon K Smyth
smyth at wehi.EDU.AU
Sat Jan 24 03:40:15 CET 2009
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
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