Interaction effects in lefse 2 between subject factors


I have a 2x3 design with 6 different groups, all between subject data. I would like to assess an interaction effect between the factors Diet (2 groups) and Genotype (3 groups). The lefse setup shows the option class and sub-class, which suggests a within subject design for the sub-class. Is this indeed the case? This is not in accordance with my study design. Is it possible to test for between subjects interaction effects in lefse?


Hello there,

For this issue I would suggesting checking out our newer tool, MaAsLin 2, which is able to handle things like interactions a bit easier. The MaAsLin 2 tutorial even addresses how to run an interaction in the tutorial. I hope this helps!


Thanks a lot for your reply and link to this R package. Did i correctly understand that in the default setting the statistics are parametric (being linear regression)? I.e. other than normalisation the non-normality of data is not accounted for?

Bests Mirjam