Accessing the MGX-normalized MTX feature expression data in MTX_model?

Infrastructure and utilities bioBakery workflows
1

Hi All,

I am using MTX_model to analyze microbiome metatranscriptomic (MTX) pathway expression data with paired metagenomic (MGX) pathway data as covariates. Is there a way to access the MGX-normalized MTX feature expression data table?

Any pointers would be greatly appreciated!
Thank you.

2

Hi there,

To get the MGX-normalized MTX data, you may need to rerun MTX_model without providing any variates (e.g. set --fixed_effects “” --random_effects “”). This process will run a simple linear model with formula: feature(RNA) ~ feature(DNA). The resulting residuals data would represent the MGX-normalized MTX data.

Thanks!
Yancong