Singularity in MaAsLin2 Linear Models

Hi, I am using LMs in MaAsLin2 to test how different variables affect microbial abundances. For some taxa, the model is showing up as Is Singular in the console as the model runs for all of the taxa. After this warning message, the code continues running and outputs all of the expected .tsv files with the model results. My two questions are:

  1. Are the results from the singular models included in the all_results.tsv automatically generated by MaAsLin2?
  2. Is there any way to flag or list the taxa for which the model is singular?
    Thank you! Happy to provide additional info if useful.

Hi @chelsea307,

Hope you are doing well. To answer your questions"

  1. Yes the results from singular models will be included in the automatically generated MaAslin2 results.
  2. This is something that has come up a few times in the lab and will be addressed in our next iteration of the tool. As for now we suggest taking a look at the log file or using the save_models parameter to save the models and manually inspect the ones of interest.

Jacob Nearing

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Thank you for your help, I appreciate it!