The bioBakery help forum

The 'covariates' parameter in 'adjust_batch {MMUPHin}'

Thanks to you for this microbiome meta analysis tool, it’s really awesome!!
I used this tool for the first time and some details are not quite clear. Here, I have a question about The ‘covariates’ parameter in ‘adjust_batch {MMUPHin}’. In the “Performing meta-analyses of microbiome studies with MMUPHin”(Performing meta-analyses of microbiome studies with MMUPHin), the covariate option only includes “study_condition”, why not add some covariates such as age and BMI to adjust the feature abundance table? (ex: … covariates = c(“study_condition”,“age”,“BMI”) … )

Any guidance would be appreciated! Thank you!

This question is hard to answer in a precise way without getting into a lot of mathematical detail, but the hand-wavy answer is: we want the adjustment step to leave the variation in the outcome variable (study_condition) intact, but adjust for inconsistency in the other covariates (age, BMI) between studies. The other covariates are used to explain the outcome in the next step (when you call lm_meta()).

Thank you so much, I know it.