betadisper in R via QIIME2 results

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1

For one of our paper, we need to calculate betadisper before PERMANOVA analysis. Is there a way to calculate betadisper statistics from qiime2 results in R or in qiime2 directly?

Thanks

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Hi @Bing,
Assuming betadisper is the same as permdisp (sorry haven’t heard betadisper), check out the beta group-significance plugin. The default test is a PERMANOVA but you can change that to permdisp easily.

  --p-method TEXT Choices('permanova', 'anosim', 'permdisp')
                       The group significance test to be applied.
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We submitted a paper and the reviewer suggested calculate betadisper in R. The comment is like this: "Homogeneity in the dispersion of the variance assumption in PERMANOVA results. Since part of the claims made by the authors are based on the results of this figure, it is critical to assess that the spread of the variance assumption is met using adequate methods."

Is this permdisp the same as the betadisper as suggested by the above reviewer?

Thanks,
Bing

5

Hi @Bing and @Mehrbod_Estaki,

The test is the same, but the visualizations are not. This older thread might be helpful as a point of discussion.

Best,
Justine

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