I'm struggling to decide whether I should split up my groups or use the contrast argument of the results function to extract the comparisons after fitting the model (as explained in the vignette). As you can see in the plot linked below, in the LI-P-L and LI-NP groups, there are a few individuals that don't cluster within their groups.
Biologically, I'm interested in comparing:
1. LI-P-L vs LI-NP 2. LI-P-L vs HV 3. LI-P-L vs LI-P-NL 4. LI-P-NL vs HV
Based on the plot, do you think it makes sense to split these into 4 separate matrices, or simply use the contrast function?
Thanks so much for your help!