I have run my samples to get alpha diversity values (using the core-metrics-phylogenetic command).
When I re-ran only a subset of my samples (using the same sampling depth), I realized that I obtained slightly different alpha diversity values for the same sample (they were slightly different for Pielou's and Shannon) . Please see photo attached for what the values were.
Would you be able to help me to figure out why this is so?
If you’re rarifying your data, your difference may simply be due to rarefaction. One way to test this is to generate 3 or 4 rarefaction instances, and look at the difference in the values. I suspect you’re going to see similar variation in the values. It looks like you’re picking the same number, and possibly same set, but the distribution in each rarefaction is different. So, if you pick 2As and 8Bs the first time and then 5A and 5Bs the second, you’ll get different values for evenness and shannon diversity, but it will have no impact on the Faiths PD or observed OTUs.
