Geometric averaging provides normalization-invariant feature ranking in compositional sequencing data (opens in new tab)

In compositional next-generation sequencing (NGS) analyses (including microbiome studies, RNA-seq and metagenomics) the arithmetic mean (AM) of relative proportions is the default operator for summarizing feature abundances. We show that this default produces unstable rankings in real compositional data. Across 102 prevalent genera in the dietswap dataset (n=38 baseline samples), 23 genera (22.5%), including members of Bacteroides, Eubacterium and Bilophila, yielded opposite group-level concl...