My Y variable is say "degradation of a certain compound x".
I have two independent variables with two levels in each, so that gives me 4 treatments. In each treatment, I have 18 replicates of a sample, and I am sampling 6 replicates at one time point.
3 time points in total.
I want to measure the differences between treatment combinations and time points. I have JMP Pro and would like to know which model fits most appropriately to my data set.
Since you are running JMP Pro, I suggest using the mixed model capability native to JMP Pro. Here's a link to the JMP online documentation for mixed modeling in JMP Pro. There are lots of examples and helpful hints.
http://www.jmp.com/support/help/13-2/Mixed_Models.shtml