Different Shannon diversity results between QIIME2 and phyloseq

Hello everyone,

as I was wondering today through my alpha diversity measures from QIIME2 and phyloseq I found differences in all my samples’ Shannon diversity measures, but curiously not in my Simpson diversity measures. I wonder why would that happen if the same table is being used in both programs. I checked samples, features abundances and they are the same, I guess the Shannon diversity formula implemented is the same either. Do you have any idea of what is going on?

I was going to check if there is a linearity between the Inverse Simpson index (1/D) calculated by phyloseq’s estimate richness, and the exponential of the Shannon index (e^H’) based on my H’ provided by QIIME2, as suggested by phyloseq’s supporting information. Right before doing it I found those differences.

I appreciate any help or insights,
Thank you,
Felipe.

Hi @Felipe_Rocha,
Please see here:

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Thanks, @Nicholas_Bokulich, I haven’t thought about the log scale used. I think it might be it.

Do you know the log scale used by QIIME2?

looks like it’s base 2: http://scikit-bio.org/docs/0.5.4/generated/generated/skbio.diversity.alpha.shannon.html

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