I am trying to figure out the best way to specify the following experiment in DESeq2.
I have a differentiation expression consisting of five conditions, the original set of starting cells (Ctrl Day 0) which are then differentiated by adding X or by a slightly different route by adding X and trt, with samples taken at two timepoints.
- Ctrl Day 0
- Diff (X) Day 5
- Diff (X) Day 10
- Diff (X+ trt) Day 5
- Diff (X + trt) Day 10
And I'm interested in asking what changes over time in both Diff and Diff + trt, and which genes are significantly different between (Diff Day 5 versus Ctrl) and (Diff + trt Day 5 versus Ctrl) and for Day 10 aswell and comparing Diff Day y against Diff Day y + trt.
I'm a little unsure how to model this properly. I've tried various ways of doing it (treatment + timepoint, and coding treatment as two variables etc) and I'm not getting anywhere and am pretty stuck.
One option is to remove the Ctrl Day 0 sample completely but this feels like the wrong thing to do.
Any suggestions? Thanks in advance,