Could you guys help me to understand my deseq2 outputs?
I used the coding 2x2 design to compare a resistant (R) and susceptible (S) plants. In this intention, we used two biological replicates for susceptible (RED – treatment, and YELLOW – control) and three replicates of resistant (GREEN – treatment and BLUE – control). I would like to know, how the controls are being used? Is the test correct the counts of treatments by control first and then compare R and S? Are the results below showing that UP means more expression on S than R and DOWN less expression on S than R?