Applying a different p-value correction (storey 's q-value)


I’ve been playing around with MaAsLin2 with my microbiome datasets. From what I understand, MaAsLin2 has various options for p-value corrections, although the one that most people use if the BH method for FDR. In looking through the options, I could find no option for FDR correction of p-values using the Storey’s q-value for an optimised FDR approach. Is this something that can be added in the future? If not, are there any modifications to the the R script which can be made to allow for FDR correction based on the Storey’s q-value?

Maaslin2 uses the built-in p.adjust() function for it’s p-value correction, so we’re limited to methods that function has available at this time. If you have a different function you’d like to use (I think you’re looking for the eponymous function in the qvalue package on Bioc), just apply that to the pval column of the results data frame from a Maaslin2 result.