I have shallow shotgun data that I am running Ancom and Ancom BC on. With Ancom i get several differentially abundant species but when i run ANCOM-BC with FDR correction, i lose all of the significant taxa.
Im wondering how to weigh Ancom vs Ancom BC and the taxa i found in ANCOM. I thought that Ancom itself had performed well at correcting for false discovery?
Thank you!
-Kevin
Hi @kkl45,
That's a great question! The methods used in ANCOM vs. ANCOM-BC are quite different, but ANCOM-BC has a more robust method for bias correction and controlling FDR by estimating the unknown sampling fractions and correcting the bias induced by their differences among samples.
I'd recommend checking out the ANCOM-BC paper to read more on the methods used:
https://www.nature.com/articles/s41467-020-17041-7
Cheers 
thank you. something i am wondering then is if i got signifincat values for Ancom but not Ancom BC how much i can trust the positive values from ANCOM?
@kkl45,
This is just my personal opinion. I would trusted ANCOM-BC findings more than ANCOM. ANCOM-BC does some corrections under the hood that could be excluding features that ANCOM finds significant. Hopefully meaning that ANCOM-BC will have less false positives than ANCOM. However, You may still consider features that have really High W scores as significant, if that's important to you. I would warn that sometimes ANCOM reports features with really low W score (Like 1) and if those are not in your ANCOM-BC results, I would say that those features are probably not truly significant.