I would like to create a design for differential gene expression analysis along the lines of
model.matrix(~0 + group + sex + batch)
but one where 'batch' is a nested variable that takes into account the library preparation batch, and the fact that some samples were re-run and the data combined to generate an adequate number of counts, AND the particular flow cells the one (or two) runs of each sample were performed on.
I have not used such a nested design before and though there is some good material I have found on the subject I am still unsure exactly how to encode such a complex nesting variable. I would very much appreciate any advice or examples that more experienced readers could provide.
Many thanks in advance!