N.not.0 column issues with CLR data

[nearinj]

Hello,

I’m linking this previous forum thread that I suspect is causing the same issue that you are encountering.

Maaslin2 N and N.not.0 output appears incorrect

Hi, I am doing an analysis with R version 4.0.2 and Maasiln2 version 1.4.0. I noticed that the N and N.not.0 columns of the results output .tsv were incorrect; specifically, they were higher than the actual N with metadata and OTU counts (i.e., the complete cases). When I removed all non-complete cases and re-ran the analysis, the N and N.not.0 were correct. Is this seemingly incorrect treatment of NA values something that has been fixed in the latest (developer) version of Maaslin2? Or will I…

Let me know if that is the case.

Cheers,
Jacob Nearing