I’d like to clarify which of Humann2’s output files are compatible with Maaslin2, and what normalization/transformations are needed. I ran multiple samples through Humann2, merged results across samples, and normalized the merged tables by both cpm and relative abundance. I then separately tried Humann2’s pathway abundance output and pathway coverage output as inputs for Maaslin2. I did not get any significant results with Humann2 pathway abundance dataset under the following Maaslin2 parameters (normalization = “NONE”, analysis_method = “CPLM”, other parameters set to default settings). However, I got significant hits with Humann2 pathway coverage data using the same set of Maaslin2 parameters.
Related to the Maaslin2 inputs and parameters I tried above, can I clarify:
- Should I be using Humann2’s pathway coverage or pathway abundance data as input for Maaslin2, and should the data be normalized by cpm or relative abundance?
- After normalizing Humann2 pathway abundance and coverage data by cpm/relative abundance, is normalization still needed for Humann2 pathway abundance/coverage datasets when used as input for Maaslin2?
- How do I determine whether to use LM or CPLM for analysis? I selected CPLM because my datasets look like there are multiple values close to zero.
Thank you for your help!
Graduate Student, UCSF