any ADVICE on transforming my microbiota dataset before ordination?

[marwa38]

[gavinsimpson]

You are likely to get better informed answers by asking the developer(s) of {phyloseq}

[jarioksa]

I have no idea what are phyloseq objects. Better ask phyloseq developers.

[eduardszoecs]

Some guidance with focus on microbio can be found here: https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.13536

I don't think that there is a one fits all method. It depends on your data, questions, methods...

[jarioksa]

These questions really are specific to the field of science and its internal traditions and rules. You better ask microbio/phyloseq communities about their recommendations. They probably differ from the ones I'd give. This also concerns Discussion #495.