I would appreciate your help with choosing the right structure of result names to answer my research question.

I defined 2 conditions:

1. Strain (WT is the reference level)
2. cell-Fraction (FractionA is the reference level)

I want to calculate the difference between FractionA and FractionB in N2, then do the same for FractionA and FractionB in the MUTANT and next to compare the FractionA-FractionB differences obtained for each strain between them.

Namely, If there was no change in the distribution of a certain transcript, then the FractionA-FractionB difference obtained for WT will be similar to that obtained for MUTANT, and the null hypothesis is that their Log2FC is zero.

My resultsNames looks like this:

"Intercept"
"Strain_MUTANT_vs_WT"
"Fraction_FractionB_vs_FractionA"
"StrainMUTANT.FractionFractionB"

I think that I should use contrast between 1 and 2 bellow:

1) Fraction_FractionB_vs_FractionA

2) c (Fraction_FractionB_vs_FractionA, "StrainMUTANT.FractionFractionB")

Does that make sense?

Thank you

For questions about statistical design, I recommend working with a statistician at your institute or someone familiar with linear models in R. I have to restrict my time on the support site to software related questions.