Hello everyone! I am currently working with WGS samples obtained from human skin for my research project, which involves performing a functional analysis and identifying differentially abundant pathways between healthy and non-healthy samples. I utilized humann 3.0 to identify gene families and pathway abundances, but I am facing challenges in determining the appropriate approach for the analysis.
Can you suggest the most suitable tests to identify the differentially expressed pathways? Should I use abundance as RPK or normalize to relative abundance? What are the optimal methods for visualizing my data?