I'm currently facing 2 independent variables to try to input on Limma to do DE analysis, but I haven't been able to. I have muscle samples with 9 different metals implanted (n=2 per metal) and a time-course (1, 3, 6 and 12 months). Here I use one of the metals as a control (since it should be inert), and I want to be able to tell the differences among metals in a specific period of time as well as see the changes with time. Is there a way to design a matrix for this experiment?
Thanks in advance