I have a microbiome dataset and I am trying to compare different groups of mice (symptomatic animals, asymptomatic animals and a control group).
I already performed some analyses with this dataset, but I am observing a great degree of individual variability among the animals. Thus, I was wondering if I could get better results by comparing only core microbiomes.
However, I am not quite sure about what whould be the best strategy to conduct such analyses. Should I use a core microbiome for all animals, or calculate individual cores for each subgroup, merge them and, then , run my comparisons?
I already performed some analyses with this dataset, but I am observing a great degree of individual variability among the animals. Thus, I was wondering if I could get better results by comparing only core microbiomes.
However, I am not quite sure about what whould be the best strategy to conduct such analyses. Should I use a core microbiome for all animals, or calculate individual cores for each subgroup, merge them and, then , run my comparisons?
