I was tring to explore the association of microbial clades with sample metadata using MaAsLin2. Three interesting fixed effects in metadata, e.g. “effect 1” , “effect 2” and “effect 3” , were running together (max_significance = 0.25 ) or separately (max_significance = 0.05 ).
But, the significnat association features I got were totally different. When I run three fixed effects together, I got less features (less than 10 features for each fixed effect based on heatmap ) compared to runing separately (more than 20 features for each one based on the Significant results).
So, which one should I use, together or separataly? which one is convinced? and why?
Hope to get your help.