Taxonomy summaries and heatmaps from rarefied or complete feature table?

[alfanon (Niccolo)]

Dear all,
I don’t understand what is best: taxonomy summaries and heatmaps should be generated from the complete feature table or on the rarefied one? Or is enough to use relative frequencies instead of rarefying?

Thanks a lot in advance for any recommendation about this

Best
Niccolò

[thermokarst]

Hey there @alfanon!

@alfanon

taxonomy summaries and heatmaps should be generated from the complete feature table or on the rarefied one?

From the complete one --- rarefaction is only necessary for some diversity metrics that are sensitive to sampling depth, otherwise, use the full feature table.

@alfanon

Or is enough to use relative frequencies instead of rarefying?

These are two different things --- relative frequencies are computed by determining the per-sample relative abundance for each feature in said sample, which can be done with or without the table having been rarefied.

[alfanon (Niccolo)]

Thanks a lot for the explanation!

Cheers

Niccolò