The bioBakery help forum

Should I report the "significant_results.tsv" as biomarkers after default run (considering q-value 0.25)?

Hi there!!!
I have run already submitted datasets with MaAsLin2 with default parameters i.e., q-value 0.25. Now, when I use q-value as 0.05 or 0.1, I rarely get any differential features.
Considering that, do you think it should be ok to report the significant features as biomarkers with q-value 0.25?

NOTE:Significant features from MaasLin output (q-value 0.25) are mostly common to that of LefSe output.


Hi @DEEPCHANDA7 - we don’t usually recommend parameter choices for project-specific analyses which are always context-dependent. Please use your judgment to decide. The flexibility of MaAsLin 2 should allow you to investigate a combination of such choices before making an informed decision based on the specific requirements of your project. Thanks!

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