[BioC] How limma Deals With Correlation Across Replicates

[Gordon K Smyth]

Matt,

A reference is given on the help page for duplicateCorrelation.

Gordon


> Date: Tue, 11 Feb 2014 13:03:23 -0800 (PST)
> From: "Matt Jones [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, matthew.jnes at gmail.com
> Subject: [BioC] How limma Deals With Correlation Across Replicates
>
>
> 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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