Hello! I’ve been running Maaslin3 and up until now it has been working great. However, I was recently given some extra metadata to work with and thus added some more covariates and have kept receiving errors. I have a microbial sample size of (n=379) with a metadata size of (n=386). I am running with 7 fixed effects and 1 random effect based on participant ID. One of those fixed effects is an ordered variable with 5 levels, while the rest of the fixed effects are all binomial. Prior to this I was running 4 fixed effects and 1 random effect. That analysis also had an ordered variable with 5 levels as one of the fixed effects.
Here are the following errors I am receiving now:
Error in add_joint_signif(fit_data_abundance, fit_data_prevalence, new_fit_data_abundance, :
Merged significance tables have different associations.
This is likely a MaAsLin 3 issue
due to unexpected data or models.
In addition: Warning message:
In formula.character(object, env = baseenv()) :
Using formula(x) is deprecated when x is a character vector of length > 1.
Consider formula(paste(x, collapse = " ")) instead.
Everything I’ve done has not fixed the issues I’m seeing. Thank you so much to who can help me with this, I really appreciate it!