I have microbioal data (S4 format created by phyloseq package), which includes an OTU table, metadata table, taxonomy table and reference sequences. I want to run anova (function adonis, package vegan) with the data and I didn't find many problems doing so, the commands worked well. However, I'm not sure if I'm doing the right way. I was told that I have to scale my data, since I have some variable columns that go from 0 to 7 at the same time that I have a column for altitude, that reaches up to 2700m, for example. In that same table I have Y/N data, name of species and infection load (values from 0.01 to 456), so different kinds of data and information. Should I scale the entire data or do I need to separate my numeric data in one table and the rest in another table and then combine them when the numeric information is scaled? Or scale in this case is not really necessary?
I also have another question, as I said I have different species - 3 more precisely - one of them has 25 samples and the other two have 157 and 115. Since adonis works with permutations, do I need to adjust the amount of samples somehow or is it already covered by the permutation step?
Thanks in advance!