Hi, I am using Masslin2 to identify taxa that are associated with specific clinical covariates (metadata) for a longitudinal dataset. I have used the patient ID as random effects and the clinical covariates as fixed effects. The tool is easy to use, and I had a few questions on the interpretation/usage of it:
Is it best to consider one metadata at a time or to consider them all together in the fixed effects, what is the difference between the two approaches?
For a categorical feature for ex. gender, if the reference gender is Male, does a positive coefficient with value of Female in significance file mean that particular taxa is positively associated with Female Vs Male; and vice versa if negative?
If one considers multiple covariates as fixed effects, I am not sure how to understand the heatmap and significance results table? For ex. I have 4 clinical sites and Gender, and the heatmap is showing positive association for 2 of the sites and Gender, but the significance results table only has one value for Site 1, how does one interpret that?
Thanks in advance!