Hello @himel.mallick ,
thanks a lot for your nice explenation in the other thread.
Regarding q-value multiple comparisons of my covariate (sequencing_depth, treatment) and my variate of interest (phenotype), I also followed the steps outlined above.
I am wondering about the results: In the original output files generated by MaAslin2, a total of 88 associations of microbes with the phenotype are found, from which 78 are significant (q-value threshold = 0.25, which is the MaAslin2 default). I am not a statistician, but I would guess this is a quite high number of significant associations?
After recalculating the q-values only for my variate of interest, if taking a q-value threshold of 0.25 as a basis, 81 associations would be significant.
Is there any rule of thumb, where one could estimate appropriate q-value thresholds?
Maybe to explain my case I am working on: Skin microbiome, 65 samples, total of 490 different species, I used min_prevalence = 0.25, min_abundance = 0.0001