Explanatory variables	Design matrix	Section
tissue LUNG, BRAIN and cells B, T	model.matrix(∼0+group) with ${\text{group}}_{LUNG\_B,BRAIN\_B,LUNG\_T,BRAIN\_T}$	Conversion to a single factor
group A, B, lane L1, L2 and technician I, II	model.matrix(∼0+group+lane+technician)	Accounting for factors that are not of interest
group A, B and batch B1, B2	Check rank of design matrix	Nested factors and matrices without full rank*
treatment X, Y and timepoint T1, T2 with repeated measurements	Model mouse IDs, then add columns representing timepoint T2 for both treatments	Time series experiment with repeated mouse measurements nested within treatments*
treatment X, Y and timepoint T1, T2 with repeated measurements	model.matrix(∼0+group) with ${\text{group}}_{X\_T1,X\_T2,Y\_T1,Y\_T2}$, and mouse ID as random effect	Treating factors that are not of direct interest as random effects*