This is a question which came up recently regarding the RNA-Seq in limma/voom, and limma/voom using the variancePartition function
When following the workflow outlined in this document (dream: Differential expression testing with linear mixed models for repeated measures) we can see at the beginning a limma/voom analysis resulting in an object called
vobj. This object was created by passing the DGEList object twice through the
voom function, once before and once after the execution of
duplicateCorrelation. The blocking factor is not provided within the design formula in both cases.
This is different to the later described
dream workflow. Here, blocking (
duplicateCorrelation) is performed as it is in the limma workflow (blocking variable not part of design formula), but when the
dream function is executed, the blocking variable is part of the design formula. Can someone briefly explain why?
A factor defining individual patient/subject effects, which are "blocked" first, seem to be provided again as random effects in the