I have a question regarding the direction of effect sizes in the comparison. My data is zero-inflated so I have problems seeing which group has highest abundance of the genus. I have groups A and B and get a positive coef (2.61) for Neisseria. Does this mean that Neisseria is higher in group B compared to group A (Since A would be the reference, alphabetically)? Please note that the group-sizes are very different, which confuses the vizualisation.
> table(pdata$Group) A B 4876 72 fit_data = Maaslin2( input_data = counts.t, input_metadata = pdata, analysis_method = "LM", transform = "NONE", min_prevalence = 0, min_abundance = 0.01, normalization = "NONE", output = "demo_output", plot_scatter=T, plot_heatmap=T, fixed_effects = c("Group"))
feature metadata value coef stderr pval name qval N N.not.zero
1 Capnocytophaga Group B 0.8479733 0.06873646 1.840022e-34 GroupB 2.189627e-32 4948 55
2 Neisseria Group B 2.6103594 0.26466737 9.770062e-23 GroupB 5.813187e-21 4948 149