[BioC] how to merge replicate spots?

[Barbara Cegielska]

Dear R-Users,

I use home-made spotted arrays and every probe is printed in triplicate. I normalized my data using limma package and I got mean from these three replicates by using duplicateCorrelation function:


design<-modelMatrix(targets, ref="HL60")
duplicateCorrelation(MAl.pAq, design, ndups=3,spacing=1)
corfit <- duplicateCorrelation(MAl.pAq, ndups=3, spacing=1, design)
all.correlations <- tanh(corfit$atanh.correlations)
fit <- lmFit(MAl.pAq, design, ndups=3, spacing=1, correlation=corfit$consensus)
contrast.matrix<-makeContrasts(AML.M2-K,levels=design)
fit2<-contrasts.fit(fit,contrast.matrix)
fit2<-eBayes(fit2)
topTable(fit2,adjust="BH")

However, this function does not change object dimmensions (plot shows all spots, not only mean from all replicates), so I try to use avedups function (a<-avedups(MA.normAq, ndups=3, spacing=1, weights=NULL)), but I have problem with creating fit2, because of differences in dimmentions. I would like to get a topTable object. What shall I do??

Regards,

Barbara Cegielska