A feasibility test for complex experiments. It's often easier to simulate the experiment to check model fits.
This R markdown notebook is a template for others to freely use. I was asked about the feasibility of running an experimental design, absorbing potential batch effects from extraction and sequencing. This Rmd script sets up the experiment, optimises what samples go in each batch to absorb each effect, and create a full rank design matrix.
Additionally, some data is simulated and two models are fit with limma.