While studying the Maaslin3 tutorial from the GitHub repository, I noticed significant associations between microbial fixed effects in the significant_results.tsv file. Could you explain why these associations appear and how should I interpret them?
Regarding the output, I’m confused about qval_individual and qval_joint. Which of these q-values should I consider for determining statistical significance in my microbiome analysis?
Hi,
I’m not quite sure what you mean with the first question. The fixed effects are the effects that will get coefficients and significance values in your output table, in the same way as if you ran a simple linear regression. Like with a standard linear regression, every coefficient gets a value and a p-value. There’s information on how to interpret the coefficients in the coef bullet on the wiki. Let me know if that doesn’t answer your question.
For qval_individual and qval_joint, it depends what you’re interested in. The qval_individual is the significance value attached to the specific abundance or the specific prevalence association, whereas qval_joint is the significance value attached to the combined abundance and prevalence association. The first one answers “is there a significant abundance association?” or “is there a significant prevalence association?” while the second one answers “is there either a significant abundance or prevalence association?” If you don’t have a preference, I’d use the qval_individual since it allows you to say whether the association was with abundance or prevalence.
Will