The bioBakery help forum

Which factor level to compare with

Hi,

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 (https://github.com/biobakery/Maaslin2), you will see that there is an option called reference which can be used to specify references for categorical variables.