I am new to DESeq2 analysis and wondered if I could get a direction about the correct design for my experiment
I have counts tables (generated with FeatureCounts)
my samples where sorted for 2 markers and I have samples from 2 different tissues (with triplicates).
I would like to know:
1 - the effect of the markers and the interaction within each tissue
2- the difference between the effect between samples
How should I approach these questions?
Should I split it into separate designs?
I am also concerned about if have enough power for multiple factor design (3 biological replicates)?