Compatible statistical analysis for SAMSA2

[Irishtsany Indira]

Dear Sam,

I want to ask about statistical analysis that is compatible with SAMSA2 pipeline. I've done annotation and aggregation and got data on functional genes & microorganisms expressed in my sample. I want to see whether giving a treatment to a sample can affect the overall functional gene expression and the overall composition of microorganisms in the sample or not. Do you have any ideas how I could do it, or do you have any idea what kind of statistical test I could use?

Thank you so much, 

Irish