Interaction term missing from Maaslin2 output

[1] ‘1.15.1’


One of my interaction variables is missing from Maaslin2 output, and I hope you guys can help me understand this and explain how to solve the problem.

I have a dataset consisting mainly of paired patient samples (“Ls_before” and “Ls_after” treatmen; for some patients there is only a single sample), but also seven female control samples. The patient samples are from both men and women.

The main variable of interest is “sampleType” (three levels: “Ls_before”, “Ls_after”, and “control”), but I also want to control for within subject correlations (using the variable “patient”) and include “Gender” as well as interaction terms for "sampleType " and “Gender”. The corresponding formula is thus: ~ sampleType + Gender + patient + sampleType:Gender

The interaction terms (“Ls_after_female” and “control_female”) have been included in the metadata table using the model.matrix function.

In the results output, I find results for all variables/factor levels except control_female (ie sampleTypeLs_after, sampleTypecontrol, GenderFemale and Ls_after_female are present).

Any explanations or suggestions are greatly appreciated.


fit_data <- Maaslin2(
    input_data = input_data,
    input_metadata = metaData_reordered,
    output = "Maaslin2_output",
    min_abundance = 0.0,
    min_prevalence = 0.1,
    min_variance = 0.0,
    normalization = "TSS",
    transform = "LOG",
    analysis_method = "LM",
    max_significance = 0.25,
    random_effects = "patient",
    fixed_effects = c("sampleType", "Gender", "Ls_after_female", "control_female"),
    correction = "BH",
    standardize = TRUE,
    cores = 6,
    plot_heatmap = TRUE,
    plot_scatter = TRUE,
    heatmap_first_n = 50,
    reference = "sampleType,Ls_before;Gender,Male"