packageVersion(“Maaslin2”)
[1] ‘1.15.1’
Hi,
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.
Sincerely,
Jan
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"
)