How to analyze ribosome profiling data in the form of a 2x2x2 experiment

Question

[kyusikkim]

Hello all! I asked this question a few years back but it seems Biostars deleted my post D:

The experiment I am analyzing has 2 strains (WT/TS), 2 conditions (A/B), and 2 "assays" (riboseq/rnaseq). I am looking to get the effect of the condition normalized for strain and RNA-seq differences. Would I be correct in assuming a 2x2x2 experiment structure and so the design I want is ~ strain + condition + assay + strain:condition:assay? Do I need to add the three dual interactions of strain:condition + strain: assay + condition:assay?

Thanks for your guys' time and help!