Hello all,

I had a question regarding making contrasts using the MakeContrasts function in Limma. I am looking to find expression differences between two strains of mice on High Fat Diet compared to Control baseline. Currently, my contrast looks like this:

cont.matrix <- makeContrasts(
  CtrlvsHFDinStrain1=Strain1HFD-Strain1Ctrl,
  CtrlvsHFDinStrain2=Strain2HFD-Strain2Chow,
  levels=design
)

Can someone validate that the makeContrasts format above is correct, but more importantly, explain the difference between making multiple contrasts at once like above rather than doing what I've included below and comparing the genes across the two resulting TopTables?

cont.matrix.Strain1 <- makeContrasts(
  CtrlvsHFDinStrain1=Strain1HFD-Strain1Ctrl,
  levels=design
)

cont.matrix.Strain2 <- makeContrasts(
  CtrlvsHFDinStrain2=Strain2HFD-Strain2Ctrl,
  levels=design
)

Thank you in advance!

Abhishek