The bioBakery help forum

Recommanded parameters when using Maaslin2 for Metabolomic data


Do you have any insights regarding the parameters to use when running Maaslin2 for Metabolomic data ?

Thank you again for your help!



Hi @NicolasB - we refrain from recommending default parameter values in general due to data-, design-, and platform-specific differences but you can take a look at the iHMP paper (Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases | Nature, Differential microbiome feature abundance) for an inspiration where we used a set of reasonable parameter values for various data types including metabolomics. I hope that helps as a starting point?

All the best,