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?