Dear All,
I have the weighted and unweighted distance matrix output file from QIIME2. I would like to find the Community structure differed significantly between the groups according to the beta diversity metrics used. How do I proceed further. I have attached a example pca plot which I am expecting.
Thank you for your help
You have a specific plugin for that in q2 called "beta-group-significance".
https://docs.qiime2.org/2019.7/plugins/available/diversity/beta-group-significance/
Just read the description in the link above and use your beta diversity output as input for the plugin.
Best,
Deni
Hi Deni Ribicic ,
Thank you so much. How do I fix the statistical test among 'permanova', 'anosim', 'permdisp'. I have equal number of sample size in three groups. We expect there will be significant difference between the groups
What do you mean by "fix the statistical test"?
You can just choose one of them as indicated in the command description.
Which test you want to choose, on the other hand, is up to you and your experimental design.
You should probably read up in literature on those tests, and explore what type of data/sample size are they best suited for.
Hope this helps,
Deni
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