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Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies.

ABSTRACT:

Motivation

Batch effects heavily impact results in omics studies, causing bias and false positive results, but software to control them preemptively is lacking. Sample randomization prior to measurement is vital for minimizing these effects, but current approaches are often ad hoc, poorly documented and ill-equipped to handle multiple batches and outcomes.

Results

We developed Omixer-a Bioconductor package implementing multivariate and reproducible sample randomization for omics studies. It proactively counters correlations between technical factors and biological variables of interest by optimizing sample distribution across batches.

Availabilityand implementation

Omixer is available from Bioconductor at http://bioconductor.org/packages/release/bioc/html/Omixer.html. Scripts and data used to generate figures available upon request.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Sinke L

PROVIDER: S-EPMC10262301 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies.

Sinke Lucy L Cats Davy D Heijmans Bastiaan T BT

Bioinformatics (Oxford, England) 20210901 18

<h4>Motivation</h4>Batch effects heavily impact results in omics studies, causing bias and false positive results, but software to control them preemptively is lacking. Sample randomization prior to measurement is vital for minimizing these effects, but current approaches are often ad hoc, poorly documented and ill-equipped to handle multiple batches and outcomes.<h4>Results</h4>We developed Omixer-a Bioconductor package implementing multivariate and reproducible sample randomization for omics s ...[more]

PMID: 33693546

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