Hello all, I have a dataset containing 4controls and infected 4 samples A brief background- I have spinal cord which i have dissected into Thoracic, cervical and lumbar regions. I have 4 animals for control and 4 for infected with 3 regions each, making a total of 24 samples. So, in short i have Control Cervical (CC), Control Thoracic (CT), Control lumbar (CL) and same goes for infected IC, IT and IL.
My main goal is to do differential gene expression between CCvsIC, CTvsIT , CLvsIL and ITvsIC. So, should i run the deseq to the whole dataset and then contrast the result against the particular groups or subset the data first and then run the deseq? Should i be including the interaction term?
AIM- To see if there is a region specific infection effect.
