PERMANOVA and Other New Features for ERGO Microbiome Analysis
/In our mission to bring the best tools to researchers, we've added new features to ERGO's microbiome analysis.
▸ PERMANOVA
Do the differences you see on the ordination plot represent a significant difference? This is one of the key questions researchers ask themselves. One way to determine significance is permutational multivariate analysis of variance (PERMANOVA), a statistical test commonly used in ecology settings [1]. ERGO uses the 'adonis' function in the R package vegan which provides functions for the analysis of ecology [2]. Each factor/condition you have defined in ERGO will automatically be tested for significance. Additionally, for ordinations each pair of levels within the factor will be tested for significance and adjusted for multiple testing using the Benjamini-Hochberg method. PERMANOVA has also been added to test significance of factors for Richness Analysis.
A table of pairwise significance tests in ERGO
▸ Centroids
For datasets with a large number of samples or datasets that appear to overlap it be difficult to see the differences. ERGO now automatically computes the centroid (geometric center) during ordinations for each level of each factor you have defined. Now you can quickly visualize differences within your datasets.
Centroids plotted in ERGO
What to give ERGO a try?
References:
Anderson, M.J. (2017). Permutational Multivariate Analysis of Variance (PERMANOVA). In Wiley StatsRef: Statistics Reference Online (eds N. Balakrishnan, T. Colton, B. Everitt, W. Piegorsch, F. Ruggeri and J.L. Teugels). https://doi.org/10.1002/9781118445112.stat07841
Jari Oksanen, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan McGlinn, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs and Helene Wagner (2019). vegan: Community Ecology Package. R package version 2.5-6. https://CRAN.R-project.org/package=vegan
