Is normalization applied before or after filtering in maaslin3?

Downstream analysis and statistics MaAsLin
1

Hi,
i found a discrepancy between the user manual and the help function in the R package regarding the order in which normalization is applied (Maaslin3 version 0.99.3):

?maaslin3 (0.99.3)
min_abundance: Features with abundances more than min_abundance in min_prevalence of the samples will be included for analysis. The threshold is applied after normalization and before transformation.

Maaslin3 user manual:
min_abundance (default 0): Features with abundances of at least min_abundance in min_prevalence of the samples will be included for analysis. The threshold is applied before normalization and transformation.

This was previously discussed also for Maaslin2 here:
Filter-normalize order and comments on tutorial?

best,
Kristian

2

Hi Kristian,

Thanks for pointing this out. I’ve updated both to the correct answer:

Features with abundances of more than min_abundance in more than min_prevalence of the samples will be included for analysis. The threshold is applied after normalization and before transformation.