ancom on metaphlan2 data

I have a metaphlan2 profile in percentage and I want to use ANCOM for statistical analyses. I saw there is a q2-metaphlan2 plugin, so I assume I am not the first person trying to use metaphlan2 profiles in qiime2.
My question is now how to deal with the zeros before using ANCOM. If I run qiime composition add-pseudocount I will replace every ‘0’ to a ‘1’ which is too much if the sum per column is 100. I have around 2 MReads/sample originally but a few only 1 MReads. Could I just multiply all hits times 200,000 to get fake counts? Or what would be the right approach?
Thank you so much for your help!

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Hi @Stef,
add-pseudocount has a --p-pseudocount parameter that allows you to adjust what you would like the pseudocount to be. So you could select something like 0.0000001 (or some other small decimal).

That said, I believe ANCOM is intended for count data, and I do not know whether or not relative abundances like you have will be appropriate for this test. :man_shrugging:

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