Hello, 

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).

meaning:

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)?

Thanks!

Do you want to model the two markers also with an interaction? Or when you said interaction were you referring to each marker with tissue?