reComBat: batch-effect removal in large-scale multi-source gene-expression data integration

Adamer, Michael F. and Brüningk, Sarah C. and Tejada-Arranz, Alejandro and Estermann, Fabienne and Basler, Marek and Borgwardt, Karsten. (2022) reComBat: batch-effect removal in large-scale multi-source gene-expression data integration. Bioinformatics Advances, 2 (1). vbac071.

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Official URL: https://edoc.unibas.ch/93727/

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With the steadily increasing abundance of omics data produced all over the world under vastly different experimental conditions residing in public databases, a crucial step in many data-driven bioinformatics applications is that of data integration. The challenge of batch-effect removal for entire databases lies in the large number of batches and biological variation, which can result in design matrix singularity. This problem can currently not be solved satisfactorily by any common batch-correction algorithm.; We present; reComBat; , a regularized version of the empirical Bayes method to overcome this limitation and benchmark it against popular approaches for the harmonization of public gene-expression data (both microarray and bulkRNAsq) of the human opportunistic pathogen; Pseudomonas aeruginosa; . Batch-effects are successfully mitigated while biologically meaningful gene-expression variation is retained.; reComBat; fills the gap in batch-correction approaches applicable to large-scale, public omics databases and opens up new avenues for data-driven analysis of complex biological processes beyond the scope of a single study.; The code is available at https://github.com/BorgwardtLab/reComBat, all data and evaluation code can be found at https://github.com/BorgwardtLab/batchCorrectionPublicData.; Supplementary data are available at; Bioinformatics Advances; online.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Infection Biology > Infection Biology (Basler)
UniBasel Contributors:Basler, Marek
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Oxford University Press
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:21 Feb 2023 13:39
Deposited On:21 Feb 2023 13:39

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