Handling zero values in metaphlan taxonomic profiles for getting residuals


I ran MetaPhlAn 4.0, and for the downstream analysis to assess the pairwise correlation between the metabolomic profiles and taxonomic profiles of my patients, I want to use HAllA. Since confounders must be regressed out separately prior to using HAllA, I was wondering what the best method is for dealing with the zero values in the taxonomic profiles output by MetaPhlAn. I have already worked with HAllA, using my raw data instead of the residuals, and I didn’t encounter any issues. I appreciate your guidance. Thanks!