[BioC] How limma Deals With Correlation Across Replicates

[Matt Jones [guest]]

Hi,

Section 11.3 of the limma User's guide introduces the concept of correlation across technical replicates. To address replicate correlation, some extra code is needed.

The sample code is given as,

> biolrep <- c(1, 1, 2, 2)
> corfit <- duplicateCorrelation(MA, ndups = 1, block = biolrep)
> fit <- lmFit(MA, block = biolrep, cor = corfit$consensus)
> fit <- eBayes(fit)
> topTable(fit, adjust = "BH")

Can anybody explain what is happening "under the hood" when the above code is executed? The user's guide asserts that this is "analogous to mixed model analysis of variance", but can somebody further this point?

Thanks.

Matt

 -- output of sessionInfo(): 

No sessionInfo().

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