Hello,
I’m also having the same issue of N_not_0 column being underestimated. I am using MaAsLin3 version 0.99.8. In the source code, the sample calculation is called after fitting the models, but I am not completely sure whether the issue is with that call or not. I am using normalization CLR and no transformation. I also wonder whether only n_not_zero amount of data were included in the models? Could you please advise?
Kind regards,
Natasha