Taxonomy summaries and heatmaps from rarefied or complete feature table?

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


Hey there @alfanon!

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

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.

:t_rex: :qiime2:

Thanks a lot for the explanation!




This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.