I am analyzing data from dental plaque microbiomes and want to see if there are any differentially abundant taxa between the 3 tooth health states. I was wondering if Gneiss would be appropriate considering that I only have 1 categorical metadata column to run the linear regression analysis on(Column title: CariesStatus with each sample being classified as: None, Enamel, or Dentin) ?
Hi @Lauren_O_Connell, you can definitely run Gneiss on it. However, Gneiss won’t explicitly tell you which microbes are differentially abundant, but rather which partitions of microbes could be explanatory.
But underneath the hood, Gneiss would be running a regression with 2 covariates (i.e. None vs Enamel and None vs Dentin) – this is how multiple categories are typically analyzed. If you need per-microbe stats, you can do this same approach with ANCOM.
Thank you much for the fast reply. Great, I understand. I will try out ANCOM for per microbe stats!