General questions about how maaslin2 works

Downstream analysis and statistics MaAsLin
1

I love this tool, thank you for developing it and for your help on this forum!

I have a couple of questions about how Maaslin2 works:

  1. for fixed effects, does it matter what order we enter them in? And if so, does the first one it chooses have a bigger impact than the others?
  2. If I have a bunch of extraneous data in my metadata file, does maaslin2 account for this in the modeling if it there are extraneous columns that I am not including as a fixed effect?

Thank you!

2

Hi @young_doktor ,

Maaslin2 uses type 3 sum of squares so ordering of fixed effects will not impact the results. Maaslin2 will not account for any data that is not included as either fixed or random effects. If no effects are included it will model a covariate for every column that in the metadata.

Thanks,
Jacob