Maaslin2 heatmap and significance_results table

I am using Maaslin2 to find associations between groups with a 2-column metadata file, sample_name and group. I use all default parameters and set reference --reference=“group,group1”. Under group there are three categories (group1, group2 and group3). If I set to --reference = “c(group,group1)”, it had errors like

Please provide the reference for the variable ‘group’ which includes more than 2 levels: group1, group2, group3.

So I suppose the program compares significant associations between groups.
However, only group2 and group3 are present in the heatmap and significance_results.tsv. I had thought group1, group2 and group3 should be in the heatmap


Thank you in advance!

Hi @XDM ,

Maaslin2 uses linear models to identify potential microbes that are differentially abundant. This is why a reference group must be chosen. In this case the heatmap that is visualized shows the coefficients associated between the reference group and the group plotted (i.e. the strength of association for group 2 in this plot shows the difference between group1 and group2). At this time Maaslin2 does not include post-hoc testing to compare two non-reference groups, however, you could compute this using standard pairwise testing.

Jacob Nearing

@nearinj Thanks for making this clear.