[BioC] limma question

[Na, Ren]

Hi,
I have some questions about the chapter 9 in limma user's guide. Please forgive my lack of statistical knowlege.
1.  For the example in section 9.4 technical replication II
>design<-designMatrix(targets, ref="wt1")
>fit<-lmFit(MA, design)
>cont.matrix<-makeContrasts(MuvsWt=(mu1+mu2-wt2)/2, levels=design)
>fit2<-contrasts.fit(fit,cont.matrix)

This technique includes an effect for each biological replicate. How about technical replicates, does it treat technical replicates as biological replicates? Am I right that this technique doesn't consider effect for technical replicate?

2. For the dye swap example in section 9.3 technical replication I
>design<-c(1,-1,1,-1)
>corfit<-duplicateCorrelation(MA, design,ndups=1,block=c(1,1,2,2))
>fit<-lmFit(MA,design, block=c(1,1,2,2), correlation=corfit$consensus)

This technique handles technical replicates by using the function duplicateCorrelation. Am I right it includes an effect for each technical replicates, but not an effect for each biological replicate? how is biological replicate's effect handled here?

I couldn't find statistician who specialized in microarray in my area, could you explain it briefly or point me to some direction to study on it? I would appreciate any help.

Ren

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