How should I choose among different methods for differential analysis?

The following guidelines are based on a paper by Weiss et al on data from 16S data.

  • DESeq2 has the highest power to compare groups, especially for less than 20 samples per group.
  • MetagenomeSeq’s fitZIG is a faster alternative to DESeq2 for large samples (over 50 samples per group)
  • For larger sample sizes (over 50 samples), rarefying paired with a non-parametric test, such as the Mann-Whitney test, can also yield equally high sensitivity.