Output data reduction

Hello Thank you very much for developing the tool, I am a newbie using MaAsLin2. I am using MaAsLin2 to correlate microbial data with clinical neuroscore data, the microbial data is zero-inflated I have processed it with CPM and rounded it to get the results of LM, CPLM, NEGBIN, ZINB models
But I have a problem: I understand that all_results will get the results of all the input strains, but in reality, all four models only get the results of more than 100 species (input strains have 1777 species), how to solve this problem?
Thank you very much!

Hi @zhoujs7,

First, apologies for the delayed response. For this issue, the only thing I can think of is that MaAsLin by default applies an abundance filter. Have you tried to turn the min. abundance and prevalence thresholds off? (e.g. = “None”)

I hope this helps, if not please let us know and if you could send some data to replicate this issue we can take a look.