[BioC] How limma Deals With Correlation Across Replicates

Matt Jones [guest] guest at bioconductor.org
Tue Feb 11 22:03:23 CET 2014


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().

--
Sent via the guest posting facility at bioconductor.org.



More information about the Bioconductor mailing list