Let's say that I have RNA seq data with multiple clinical conditions from multiple patients/samples. As far as I understand, the first level that is used is the reference level that other conditions will be compared to. For example if I have the following conditions: 1. Control 2. Treatment 1 3. Treatment 2
One option is to put the "control" as the first level that the other conditions will be compared to separately: Treatment 1 vs control Treatment 2 vs control
The question: If I want to compare the treatments (i.e. Treatment 1 vs Treatment 2), what's the level that should be run first as the reference level?