Does the order of the samples matter in the design matrix? (paired samples - limma package)
When setting up the design matrix that will be used to fit the linear model for differential gene expression using the limma package, is it necessary that each two paired samples be right next to each other in the matrix? (e.g. 1_a 1_b 2_a 2_b ...) Or does it still work when the paired samples are not next to each other? (e.g. 1_a 2_a 3_a 1_b 2_b 3_b ...)
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No, it does not matter. It would be mentioned in the limma manual if it was.
Alright, thank you for your reply.