Maaslin2 significant results


I ran maaslin2 on some microbial relative abundance data but I am confused about the results. In the significant results table I only see the following taxa that are significantly associated with my variables of interest (control vs treated and pre vs post randomization).

However, when I open the all results table there are two additional taxa that have p-values <0.05 (highlighted in yellow) that are not in the significant results table. Can someone please explain this?

Thanks for the help in advance.


Hi! The default settings are for Qvalue less than 0.25; That explains your discrepancy between all and significant results

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Thanks @lalas25! I also found one taxa with a p-value >0.05 highlighted below. what is the default cut off for p-values?

The q-value for maximum significance is the only editable parameter with the flag max_significance. So if it is under 0.25 (by default) it will make the significant results list even if p value is greater than 0.05

My understanding is the q-value is generated from p-values that are below 0.05 for BH FDR method. So Iā€™m not sure I understand how/why it is included in the significant results list.

Nvm I realize that was a silly question now since the qvalue is generated for all features. Thanks for your help @lalas25!