Maaslin2 significant results

Downstream analysis and statistics MaAsLin
#1

Hi,

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).

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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?

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Thanks for the help in advance.

Alya

#2

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

1 Like
#3

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

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#4

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

#5

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.

#6

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