shannon entropy

[Nicholas_Bokulich]

Hi @Sue

@Sue

Could this discrepancy be considered normal? Is it possible that this difference arises from using different tools or methods to calculate the Shannon entropy?

Most likely yes. Shannon entropy can be calculated with different logarithmic bases, and different tools will use different bases by default, which can lead to such a discrepancy when comparing estimates from different tools, or when comparing to literature.

Many other things will also impact the discrepancy in literature, e.g., different sequencing technologies, molecular targets, etc.

There is a little more discussion of this in this topic, I suggest reading there for more details:

shannon index value

Hello Ana, A bunch of things can affect the Shannon index. Switching from OTUs to ASVs can change it. The Shannon index uses a log scale, but it can use log2 or log10 or natural log, and all of these are perfectly valid nobody EVER reports which one they are using! This sounds crazy. And it is. And yet if you look in the original Shannon entropy paper that has 69,200 citations, all three of these log bases are mentioned on page one: The choice of a logarithmi…

I hope that helps!