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Frequently Asked Questions (FAQ)

1. What is ComBatFamQC?

ComBatFamQC is an R package designed for batch effect diagnostics, data harmonization, and post-harmonization analysis in multi-site studies.
It helps identify and correct unwanted site or scanner effects while preserving biological signals.

2. Can I use ComBatFamQC without R?

Yes. The package includes command-line scripts that can be run directly in your terminal for automated or large-scale processing.

3. What harmonization methods are supported?

ComBatFamQC integrates four type of first time harmonization methods: Original ComBat, Longitudinal ComBat, ComBat-GAM, CovBat In addition, ComBatFamQC supports out-of-sample harmonization using ComBat and CovBat, allowing new data to be harmonized based on previously fitted models.

4. What input data format is required?

You’ll need:

• A feature matrix (subjects × features; e.g., cortical thickness, volume, or connectivity)

• A metadata file including the batch variable (e.g., site/scanner) and relevant covariates such as age, sex, and diagnosis.

Get Support

If you have a question about this package, please open an issue on GitHub. The maintainers will be notified about your post and will respond when they’re able.

If you have used ComBatFamQC in your research and would like to share a summary of your work as a blog post on this website, please open an issue. The maintainers will collaborate with you to create and publish your post.

Last updated: November 2025