2.7. CoDa Analysis of Gut Microbiota
The experimental matrix used for CoDa analysis, obtained from The first issue is usually addressed by normalisation before the analysis, but treating the data set as compositional does not require this pre-treatment. Regarding the second aspect, the total count constraint induces a strong dependence on the abundance of taxa (the increase in one taxon decreases the counts of others since their total number cannot exceed the sequencing depth specified). CoDa analysis adequately addresses this feature, minimising its effect in this work. The high proportion of zeros (sparsity) is considered zero counts and handled according to the package or program manuals. Usually, they are replaced by the values imputed using the Bayesian-Multiplicative (BM) treatment, as proposed by Palarea-Albaladejo and Martín-Fernández [Among the conditions required for a proper CoDa analysis are permutation invariance, scale invariance, and sub-compositional coherence, since one usually works with sub-compositions [