I am new to microbiome data analysis.
The microbiome data I have is from 80 specimens which upon analysis produced 116 consensus bacterial species. While I was trying to calculate the Chao-2 richness index and Simpson’s diversity, I obtained values for each specimen. How can I populate it as one value? Do I average it or anything like that?
Can you expand a bit on what it is you are trying to do? Also, is this 16S data, what do you mean by consensus bacterial species?
Chao and Simpsons index are alpha diversity metrics. These represent within sample diversity and as you indicated they are a single value. So, much like any other trait (weight, height, age etc.) you can average them based on your grouping of your choice. It really depends on what your biological question is.
Chao2 is not something that is calculated with any Qiime2 plugins I’m aware of, are you doing your analysis outside of Qiime2? It would be good to know as this can help us point you to the right sources.