RSim: A reference-based normalization method via rank similarity
Fig 3
Compositional bias can create false clusters in PCoA plots.
In (a) and (b), samples are randomly divided into two groups. No modification is applied to (a), while the count data in group 1 is rarefied in (b). In (c), samples are divided into two groups based on the sequencing depth (>10000 belongs to the first group, and <5000 belongs to the second group). In these figures, RSim normalization can help remove the false clusters resulting from compositional bias. Euclidean distance with log transformation is used in all PCoA plots.