MultiBaC: an R package to remove batch effects in multi-omic experiments
Manuel Ugidos1,2, María José Nueda3, José M Prats-Montalbán2
1Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia 46010, Spain.
Motivation:
Batch effects in omics datasets are usually a source of technical noise that masks the biological signal and hampers data analysis. Batch effect removal has been widely addressed for individual omics technologies. However, multi-omic datasets may combine data obtained in different batches where omics type and batch are often confounded. Moreover, systematic biases may be introduced without notice during data acquisition, which creates a hidden batch effect. Current methods fail to address batch effect correction in these cases.
Results:
In this article, we introduce the MultiBaC R package, a tool for batch effect removal in multi-omics and hidden batch effect scenarios. The package includes a diversity of graphical outputs for model validation and assessment of the batch effect correction.
Availability And Implementation:
MultiBaC package is available on Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/MultiBaC.html) and GitHub (https://github.com/ConesaLab/MultiBaC.git). The data underlying this article are available in Gene Expression Omnibus repository (accession numbers GSE11521, GSE1002, GSE56622 and GSE43747).
Supplementary Information:
Supplementary data are available at Bioinformatics online.
