I am using Maaslin2 to find assocation between taxa with a few metadata, I set age, gender, BCcat as fixed_effects. Under BCcat there are three categories (NC, PN and UC), I set reference = “BCcat, NC”.
So it means compare PN and UC with reference to NC.
However, BCcat NC is present in my heatmap. Can anyone enlighten me why is it so? I thought BCcat PN and BCcat UC should be on the heatmap instead if there is any significant association?
Thank you in advance!