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!