I would also add a clarification to your interpretation of the PERMANOVA test. As stated in the tutorial, the PERMANOVA will
test whether distances between samples within a group, such as samples from the same body site (e.g., gut), are more similar to each other then they are to samples from the other groups (e.g., tongue, left palm, and right palm)
This is slightly different than “seeing if a PCoA plot clustering is significant” because the PCoA plot is an approximate representation of the distances between samples.
Let me know if I can provide any more clarification!
Thank you so much for pointing towards the tutorial. I just did it. I think I have a comfortable idea how to do the PERMANOVA. The only problem I have now is the “Data File” format. Let me explain below:
Q2 secret: you could also use qiime sample-classifier metatable to import and convert a TSV directly to a feature table. This method was designed for merging metadata into feature tables for specific purposes but if you only input a TSV format observation matrix it will do the conversion and import in one go.
Thank you so much @Nicholas_Bokulich. That command of passing the .tsv feature table as metadata and not providing the source does import the file as .qza and I was able to do my first PERMANOVA test on QIIME2 after that. I guess this thread can closed as “Solved”.