sample-classifier support for presence/absence tables

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1

Hi! Sorry if this is a duplicate but I have searched through the forum and can't find an answer to this question:

I have been trying out the qiime2 sample-classifier methods as an alternative to running classifiers with different R packages.

I'm wondering why the methods implemented by this plug-in require FeatureTable[Frequency] artifacts and don't accept presence/absence or relative abundance data?

If I import a presence/absence table as a FeatureTable[Frequency] artifact the methods seem to work fine, but I am worried that I am violating assumptions somewhere in the method and can't be sure.

Thanks for any advice/help!

2

Hi @matt_rogers ,

No you are not breaking any assumptions. This is something that has been on the to-do list to add, but just at low priority so it has not happened yet. It would be an easy fix if you would like to contribute to the q2-sample-classifier plugin source code :wink:

In the meantime, your workaround should be fine (just don't use that fake frequency table for anything else! Because for most other methods it would break assumptions!)