Interaction and transformation to deltas

Downstream analysis and statistics MaAsLin
3

Hi @himel.mallick, thank you for your message. Before opening this topic, I had already read the messages, but I still don’t seem to get significant results with my data for the interaction variable, that is, ‘GroupB:TimeFinal’ does not appear in the ‘metadata’ column of the results, even when changing the data to increase the differences in Blautia abundance between the groups after the intervention. For this reason, I am requesting assistance with my case:

fit_data <- Maaslin2(input_data, 
                                input_metadata, 
                                output = 'demo_output',
                                random_effects = 'Subject',
                                fixed_effects = c('TimeFinal', 'GroupB', 'GroupB:TimeFinal'),
                                standardize = F,
                                min_abundance = 0,
                                min_prevalence = 0.1,
                                analysis_method = "LM",         
                                normalization = "CLR", 
                                transform = "NONE",
                                max_significance = 0.15)

fit_data$results

Additionally, I have tried to perform the analyses with the deltas, after subtracting the basal abundance from the final, but the model does not run, and I don’t understand if there is a specific aspect of the parameters to consider when the data is transformed into deltas. I would appreciate any example or comment on this matter.

Best regards,
Bruno