1 Motivation

In many cases it is useful to test for differential abundance of sequences/taxa between two (or more) groups of microbiome samples. This is inherently a multiple comparisons/testing scenario, and so the same corrections for multiple testing that we learned in the previous section apply here. Many of the workflows will perform this correction by default.

 


2 Goals of this Lab

The goal of this lab is to practice executing a few different workflows for differential abundance multiple testing (DESeq2, edgeR, metagenomeSeq), and combining their output into a single graphic (ggplot2, gridExtra).