STAMP
Statistical Analysis of Metagenomic Profiles
STAMP Extended Error Bar plot
Learning Objectives
Develop testable hypotheses about metagenomic datasets.
Analyze metagenomic datasets using statistical software.
Explain the difference between statistical significance and biological significance.
Define the following key statistics terms: effect size, confidence interval, p-value.
Analyze microbial composition data about samples from different environments.
Interpret heat maps, ordination plots (e.g. Principal Coordinate Analyses), and extended error bar plot, and other data visualizations.
STAMP software package allows for the quantitative analysis of taxonomic and functional profiles, and generates data visualizations to support such analyses. It can be used for exploratory analysis using such things as Principal Component Analysis and heatmaps, as well as analyses to investigate the statistical significance (p-value) and biological relevance (effect size/confidence intervals) for comparisons.
The STAMP User’s Guide is available as a separate document, and it does an excellent job explaining STAMP’s data visualizations and statistical tests. Additional instructional materials, including readings, slides, and a video tutorial are available in the PUMAA
Tutorials
Detailed instructions are available in the PUMAA Manual: Activity 3
