Basic logic and use of PERMANOVA for microbiome data
Entering edit mode
21 months ago
xgeneral57 ▴ 10

PERMANOVA is frequently used in microbiome studies when analyzing beta diversity. While I know that basics of PERMANOVA are similar to ANOVA (with some differences related to permutation), I have a hard time understanding the logic of this analysis in the context of beta diversity analysis. - In particular, we perform statistical tests for vectors of data, e.g., to compare the abundance of OTU X in cases vs. abundance of OTU X in controls. When working with beta diversity though we deal with a distance matrix (e.g. based on Bray-Curtis) for pairs of samples and not vectors. Can someone please explain to me what quantities are compared against each other using PERMANOVA?
- Should one compute different distance matrices for each category (e.g., one for cases and one for controls) or just one matrix that includes samples from all categories? Many thanks!

microbiome statistical test • 1.9k views
Entering edit mode
13 months ago

A bit late but might help anyone. We use PERMANOVA to compare centroids of groups of samples, usually represented through PCoA or NMDS. The matrices visualized are usually beta-diversity indexes previously obtained. Thus, there is no need to calculate multiple matrices, as one matrice will hold the beta-diversity measure for all samples, for that reason a meta-parameter is usually provided (i.e. treatment). At last, the significance of centroids can be accessed by p values.


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