Fig. 5
The effect of normalization, transformation, and distance metric on beta-diversity separation. a Datasets B1–B3 (vertical panels) with all combinations of library size normalizations (horizontal panels) and count transformations (color) applied prior to the calculation of distances and use of Adonis permanova model. Effect of design variable in question (B1—age; B2—tongue versus palate; B3—age group) measured as model R 2 value. The highest and lowest R 2 values (yielding best and worst separation, respectively) are demonstrated in subplots b–g for each dataset as principal coordinate analysis plots, colored by design variable, with overlaid prediction ellipses (B1—subplot (b, c); B2—subplot (d, e); B3—subplot (f, g)). CSS cumulative sum scaling, TMM trimmed mean of M values, TSS total sum scaling