I have multiple conditions each with multiple mutants and their own wild types. Each sample has been sequenced using 2 different methods. I've been trying to work out if it's feasible to compare samples to their wildtypes then do a comparison between comparisons.

Currently, I've been using contrast to compare mutants and wild types manually. I was wondering if there's a way within deseq to find the difference for each gene between 2 conditions? e.g. compare the difference between 1 mutant and its relevant control with another mutant and its control.

Sorry if this should be obvious.