Hi, I have a question about ANCOM-BC output after running the QIIME2 plugin. Specifically, in reporting statistically significant absolute abundance differences, would it be appropriate to report p-values from the tabulate file, or do q-values have to be reported? I understand that the q-values are the values after multiple corrections, but are the p-values also useful? I have many ASVs that are significant by p values but not by q values. Thank you for any insights!
Ancom-bc, as many other differential abundance tests is designed to test if abundances of numerous features are differ between certain groups. Since numerous features are tested, there is a burden of multiple tests, and chances of significant p-values, obtained by a chance increase with number of features. So I would only report q-values as significant.
Though, there are some tests, like LEfSe, that do not correct for multiple tests by default.
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