which FDR/q-value is recommended for meta-genome?

[Khemlal Nirmalkar]

Hello Microbiome helper Group,

                                                     I am a little bit doubtful regarding FDR/q value. In Maaslin the cutoff q value is 0.25 but in some other meta-analysis, FDR/q-value/p-adjust value is 0.05.

Please kindly suggest which one is better to consider.

Thanks,

Sincerely,

Khem

[Gavin Douglas]

Hi Khem,

Selecting a q-value cut-off just comes down to what false positive rate you are willing to accept. If you are performing an exploratory analysis interested in identifying many putative biomarkers than using a less stringent cut-off might make sense. However, if you want to restrict your results to only biomarkers you have confidence in then a lower cut-off of 0.05 or 0.1 is typical. The important thing is that you clearly describe the cut-off you selected and how this might affect the interpretation of your results.

Best,

Gavin

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[Khemlal Nirmalkar]

Dear Gavin,

                 Thank you so much for your useful comments.

Khem