Hi.
Just wondering the reason why q-value default parameter is 0.25
Is it acceptable to consider differential abundant features using q-value default parameter?
Thanks
I have the same question. I have read and understood that q-values are always context dependent but wondering why it has been set to 0.25 by default. The paper mentions FDR<0.25 as well. @himel.mallick Could you please guide us on the matter?
Hi @zubairkhalid - it has been set to 0.25 by default because MaAsLin 2 expects a multivariable model with a few covariates adding to the multiple testing burden compared to conventional univariable differential analysis where a default value of 0.05 is more common. Hope this makes sense.
Many thanks,
Himel