Tutorials
Typical Workflow
The ComBatFamQC workflow guides users from raw multi-site data to harmonized, analysis-ready results. You can run the full workflow using the R Shiny app or the command-line interface.
1. Data Preparation
Start with your unharmonized dataset that includes:
- A feature matrix (e.g., cortical thickness, volume, or connectivity)
- A metadata file containing covariates such as site, age, sex, and diagnosis
2. Batch Effect Diagnostics
Detect and measure site-related variation using interactive plots and statistical tests, including:
- Interactive Plots: Residual Box Plots, Exploratory Density Plots, PCA/t-SNE Plots
- Statistical Tests: ANOVA, Kruskal-Wallis, Levene’s, Bartlett’s tests
These diagnostics help determine whether harmonization is required and which method to apply.
3. Harmonization and Post-Analysis
Apply one of four harmonization methods (ComBat, Longitudinal ComBat, ComBat-GAM, or CovBat) to remove site effects while preserving biological variability. After harmonization, reassess batch effects, explore age trends, and generate residual datasets for downstream analysis.
The interactive workflow can be found below:
Click a node above to display a related figure here, or click an edge to see its explanation.
Tutorial Videos
Interactive Batch Effect Diagnostic
Data Overview
This video introduces the ComBatFamQC interface and data structure, showing how input data are organized and prepared for harmonization.
Summary
An overview of key summary statistics and visual outputs generated after harmonization, illustrating how ComBatFamQC evaluates data consistency.
Residual Plot
This tutorial explains how to interpret residual plots to assess whether batch effects remain after harmonization.
Diagnosis of Global Batch Effect
Learn how to identify and visualize overall batch effects across datasets, helping ensure harmonization quality at a global level.
Diagnosis of Individual Batch Effect
This video focuses on assessing individual batch-level differences and detecting potential sources of variation after correction.
Interactive Harmonization
Explore how to use the interactive ComBatFamQC interface to fine-tune harmonization parameters and visualize real-time effects.
Post-harmonization Analysis
Interactive Life Span Age Trend
This tutorial demonstrates how to visualize age-related changes across brain regions, highlighting lifespan trends using interactive plots.