Hello all,

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

The experiment you describe is similar in structure to that in your previous post

https://support.bioconductor.org/p/121009/

and you can use the same method as before. Previous you had 2 genotypes x 4 time points, now you have 9 metals x 4 time points, but that doesn't cause any complication. Exactly the same approach will work as before.

The fact that one of the metals is a control has no effect on the design matrix, it only affects which comparisons (contrasts) are of interest to you.