The bioBakery help forum

Which factor level to compare with


I want to find the associations of taxons with disease status (two status, Non-critical/Critical). And at the same time, I also have healthy controls. I ran MaAsLin, and the result seems to be always compared to Critical status. But i want to compare among these three groups or both compared to Healthy controls? How should i prepare the input?

Hi @Qiuyu-dot - this is something we have recently added. If you install the latest development version from Github (, you will see that there is an option called reference which can be used to specify references for categorical variables.