# Procrustes analysis: p-value
**URL:** https://forum.qiime2.org/t/procrustes-analysis-p-value/9184
**Category:** Ideas and Suggestions
**Created:** [April 9, 2019, 3:13pm UTC](https://forum.qiime2.org/t/procrustes-analysis-p-value/9184 "2019-04-09T15:13:35Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@bsen2018](https://forum.qiime2.org/u/bsen2018)
#### Post date: [April 9, 2019, 3:13pm UTC](https://forum.qiime2.org/t/procrustes-analysis-p-value/9184/1 "2019-04-09T15:13:35Z")
Hello!
I was recently testing the Procrustes analysis in Qiime2 using these two methods: [procrustes\_analysis](https://docs.qiime2.org/2019.1/plugins/available/diversity/procrustes-analysis/?highlight=procrustes) and [procrustes\_plot](https://docs.qiime2.org/2019.1/plugins/available/emperor/procrustes-plot/?highlight=procrustes). The plot was generated successfully. Yet, it would be nice if we can also obtain the p-value for the statistical significance of the observed object separation congruency, subsequently. It seems Qiime1 could generate the p-value through a [Monte Carlo simulation](http://qiime.org/tutorials/procrustes_analysis.html). Is there a workaround in Qiime2 for generating the p-value? I would suggest that a method is included to generate the p-value. Thanks!
---
### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [April 9, 2019, 8:26pm UTC](https://forum.qiime2.org/t/procrustes-analysis-p-value/9184/2 "2019-04-09T20:26:43Z")
HI @bsen2018,
Have you checked out the [mantel test](https://en.wikipedia.org/wiki/Mantel_test) (`qiime diversity mantel`)? That's my go to for showing that two distance matrices are correlated!
Best,
Justine
---
### Author:  [@bsen2018](https://forum.qiime2.org/u/bsen2018)
#### Post date: [April 10, 2019, 2:33am UTC](https://forum.qiime2.org/t/procrustes-analysis-p-value/9184/3 "2019-04-10T02:33:59Z")
Hi @jwdebelius, thanks for the suggestion. Yes, I do use mantel test quite often but it has several drawbacks as discussed by Pierre Legendre. More importantly, procrustes analysis (PA) provides a better visualization of the object congruency and serves the specific objective of the study. I noticed that @Nicholas_Bokulich used the PA in one of his paper on [quality filtering](https://www.nature.com/articles/nmeth.2276#supplementary-information) and included the p- value, which was indeed an apt approach.
---
### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [April 10, 2019, 12:14pm UTC](https://forum.qiime2.org/t/procrustes-analysis-p-value/9184/4 "2019-04-10T12:14:18Z")
I tend to use procrustes for global patterns and visualisations, and I advocate that, but for p-values, I prefer mantel for my correlations. That said, I clearly need to re-read Legrande & Legrande again, thank you for the suggestion!
---
### Author:  [@bsen2018](https://forum.qiime2.org/u/bsen2018)
#### Post date: [April 10, 2019, 1:48pm UTC](https://forum.qiime2.org/t/procrustes-analysis-p-value/9184/5 "2019-04-10T13:48:27Z")
Hi @jwdebelius,
I compared the p-values with the [protest](http://labs.eeb.utoronto.ca/jackson/pro3.html) and mantel functions in the vegan package (R), and it turns out that they are different for the same two OTU tables. Since the [underlying algorithms](http://labs.eeb.utoronto.ca/jackson/pro4.html) are different for these outputs, it would be nice if the p-value and the Procrustes sum of squares are outputted in Qiime2 PA. In my opinion, it may also not be appropriate to include the p-value output of the Mantel test to support the PA results. Moreover, we are not quite certain if the algorithm/steps for the [pcoa](https://docs.qiime2.org/2019.1/plugins/available/diversity/pcoa/) (bray distance based) in Qiime2 is the same as the cmdscale (bray distance based) function in R. Also, I am not sure if pcoa method in Qiime2 does any sort of data transformation (e.g., log transformation etc.) or not. 🧐