ANCOM-BC2 returns ASV and not Genus despite argument "rank = "Genus"

[gkuhlenbaum]

Dear Sir,

I ran ANCOM-BC2 previously using the argument "rank = "Genus"" and the result (result$res) contained in the first column the names of the taxa (e.g. "Genus:G__Faecalibacterium"). Now, I had to update Bioconductor to version 3.22 and also ANCOM-BC2 to 2.11.1 (unfortunately I did not write down the previous version). When I now run exactly the same script that gave me the taxa as "Genus:G__my_genus" it now gives me the taxa as "ASV_141". I tried to circumvent this using tax_glom() first to agglomerate at taxon level but the result is not the same as the previous version of ANCOM-BC2 with argument "rank = "Genus"" and without previous agglomeration. I guess this might be due to different ways the argument "prv_cut" is applied to agglomerated vs. not agglomerated data. However, as I gathered form the information about ANCOM-BC2 the recommended way is to leave agglomeration to ANCOM-BC2 and not work with pre-agglomerated data. I tried to find the Genus names using str(result_of_ancom) but I could not find them...

I attach a working example consisting of a short R-script and the data as ".rds". The example works on my computer. However, the results give taxa as ASV's.

I would be very grateful if you could help me with this.

Yours sincerely

Gregor
gregor.kuhlenbaeumer@uksh.de

ancom_problem.zip

[taknotts]

I am having a similar problem. The issue of the result output taxon with the OTU name instead of name from tax table occurs for the lowest level in my tax table- species. The same code used to work.