I have RNAseq data from 4 samples with 3 replicates each:
Treated A, Vehicle A, Treated B, Vehicle B,
I have defined sampleCondition as T or V and sampleGroup as A or B and created a sampleTable accordingly. I am interested in obtaining results for the differentially expressed genes due to treatment in group A and B (TA vs VA and TB vs VB), as well as the differentially expressed genes in the groups, treatment aside (VA vs VB and TA vs TB).
I'm unsure how to define design so I can obtain these comparisons? I suspect it may be design=~group + condition + condition:group?
Additionally, I'm unsure how I should write results() in order to obtain the specific data comparisons.