Fig. 2

PCoA patterns of technical and biological variation. Two groups (black, gray) with significantly different distances (P < 0.05) and varying effect size. a A large separation in PCoA space and large effect size. Separation in PCoA space (shown here in the first two dimensions) may be caused by technical differences in the same sample set, such as different primer regions or sequence lengths. b Clear separation in PCoA space, similar to patterns seen with large biological effects. In cross-sectional studies, age comparisons between young children and adults or comparisons between Western and nonWestern adults might follow this pattern. c Moderate biological effect. d Small biological effect. Sometimes effects can be confounded. In e the technical effect and in f the biological effect are conflated because the samples were not randomized. In g and h, there is a technical and a biological effect, but the samples were randomized among conditions, so the relative size of these effects can be measured