I have 4 sets of sequenced data of water samples. Each sample set has 10 samples. Can you please let me know how can I perform p-value and std deviation analysis from the data generated by QIIME analysis. I have performed all analysis from QIIME like, taxa composition, beta diversity, core-metrics to get an idea of the diversity and composition of bacterial communities in water samples. the reference paper is this:
If you want to perform a differential abundance test, you can use qiime composition ancom (see the tutorials at qiime2.org for examples, e.g., the “moving pictures” or “parkinson’s mouse” tutorials both use ANCOM).
There is also a new differential abundance plugin that joined the QIIME 2 family ():
LEfSe is not part of QIIME 2 — if you want to use LEfSe you should check out the appropriate manual or post to the LEfSe forum to learn more about formatting for that method.
Thanks @Nicholas_Bokulich. I understand ANCOM does not return P-values, I already read about it. I wanted to know if you could suggest how can I get P-values for each sample, so significance across the sample sets can be assessed? thanks.