Does anyone know what the cutoff value default is for ANCOM run within QIIME2? For example, on ANCOM run in R, the user may specific common cutoff of 0.7, or more restrictive 0.9 (GitHub - FrederickHuangLin/ANCOM: R scripts for Analysis of Composition of Microbiomes (ANCOM).).
What is the cutoff being used in ANCOM in QIIME2?
Thank you for your help!
Hi @hpyle50 ,
The QIIME 2 implementation of ANCOM is still based on the original code which tried to calculate that threshold on the fly and did not have fixed values like the newer versions do. This approach has some benefits but can often yield odd results as discussed before on this forum. You can see a bit more on this specific issue here.
Hope that helps!