I have 12 samples - 3 Controls, 3 T1 , 3 T2 and 3 T3. I am interested in looking at genes that are different between controls and treatment. Also I would like to obtain DE genes that are different between control average and treatment average for which I had provided the contrast above that I want from the analysis (T1 + T2 + T3)/3 - Controls. I am unable to input such contrasts in the test_differential_abundance function under the contrasts argument. Can you suggest the design and contrasts arguement for looking at control vs treatments and controls average versus treatment average.
Thank you Adi