Results have variable name as value

[nearinj]

Hi Samantha,

I’m going to link you to this explanation by @himel.mallick (one of the original authors).

MaasLin2 missing value in the metadata

Hi there, I am using MaasLin2 to test the association between taxonomy and binary clinical outcomes. In the metadata clinical outcomes, I have several missing values (shown as “NA”). After I ran MaasLin2, the output file still showed the total number of samples, i.e., not removing samples with NA values. And in the box plot for showing significant taxonomy association, in addition to 0 and 1, there is another box for NA. It seems MaasLin2 can remove missing values automatically when performing …

In essence during model fitting the models will not use any data that is missing values in the covariates. If you want to avoid this you could try imputing them in sensible manner or modeling the lack of data directly (although this could be messy depending on the data etc.).

thanks,
Jacob