Hello Stefano,
in the pipeline you can use contrasts for the test_differentialabundance() to extract the comparison you are interested in. When using a formula with interaction (e.g. treatment*genotype), you create columns with colon (treatment:genotype) and limma::MakeContrasts does not accept it. If you manually modify the design matrix by exchanging : with the function works.
Cheers,
Alex
Hello Stefano, in the pipeline you can use contrasts for the test_differentialabundance() to extract the comparison you are interested in. When using a formula with interaction (e.g. treatment*genotype), you create columns with colon (treatment:genotype) and limma::MakeContrasts does not accept it. If you manually modify the design matrix by exchanging : with the function works. Cheers, Alex