Hello Colin,

Thank you for this explanation again!

However, I am still a bit confused in the order. Please let me know if I have interpreted this the correct way or not:

When looking at the PD mouse tutorial adonis:

qiime diversity adonis

--i-distance-matrix core-metrics-results/unweighted_unifrac_distance_matrix.qza

--m-metadata-file metadata.tsv

--o-visualization core-metrics-results/unweighted_adonis.qzv

--p-formula genotype+donor

By putting genotype first in the formula (genotype + donor, not donor+genotype) I adjust for donor to see if genotype will still have an effect.

So if I want to analyse the effect of treatment on my chickens I should write the formula line like this: --p-formula treatment + room.

And if I want to analyse the effect of room I do it the other way around.

is this correct?