The bioBakery help forum

Maaslin2 model validation

Dear all,

What would you recommend for Maaslin2 model validation?

Normally, one of the key steps is to plot the residuals against the fitted values and I guess one could do that for each of the ASVs, but Maaslin only returns the residuals and not the fitted values (which may have been transformed/normalized).



Hi @Ricardo_Ramiro - you can use the residuals to make a per-feature QQ plot as a visual inspection (see, e.g. Another way would be to randomly shuffle the dataset (possibly many times) and construct a similar QQ plot based on the shuffled p-values (which should closely follow a uniform distribution under the null). Hope this helps.

Hi @himel.mallick

Thanks a lot for your reply. That helps and could be easily done. I guess I was more wondering about plots of fitted values against residuals, to check for problems in variance. Is there a way to also extract the fitted values (post-transformation/normalization)?

Hi, @Ricardo_Ramiro- I just pushed an update in GitHub which ensures that you get the fitted values along with the residuals as output.

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Hi, @himel.mallick - just a follow-up to the above thread. I’ve just re-installed the R package and still do not seem to get the fitted values as an output? Just wondering if there is anything else I need to do, or specify to get this output. Thanks very much!

Hi @CHall - if you install the latest version from GitHub, you should be able to see fitted.rds in the output folder. Let me know if you still don’t see it after re-installing.