Feature ID's as Independent Variable

Downstream analysis and statistics MaAsLin
1

Hello! We are interested in how the microbiome relates to social behavior. However, we want to have social behavior as our dependent variable and the microbiome as a fixed effect. Is there a way to do this in MaAsLin2? Or does MaAsLin2 only allow for the microbiome/feature IDs to be the dependent variable?

This is our current model (“degree_log10_std” is our measure of social behavior that we want to have as the dependent variable).

fit_data ← Maaslin2(
input_data, input_metadata, ‘maaslin2_output/degree’,
fixed_effects = c(‘degree_log10_std’,‘group_size’,‘age’,‘valley_position’,‘sex’),
random_effects = c(‘uid’,‘year’),
normalization = “CLR”,
standardize = FALSE)

Does anyone know how to make “degree_log10_std” the dependent variable and feature IDs a fixed effect? Thank you so much!

2

This is something we’ve discussed for Maaslin3 but is not planned for Maaslin2. You might find it useful to run Maaslin2 for the normalization/transformation, then pass the processed data to a different model of your choosing.

3

Thank you so much @andrewGhazi! I really appreciate your time and help.