Introduction

Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. There are several existing batch adjustment tools for '-omics' data, but they do not indicate a priori whether adjustment needs to be conducted or how correction should be applied. We present a software pipeline, BatchQC, which addresses these issues using interactive visualizations and statistics that evaluate the impact of batch effects in a genomic dataset. BatchQC can also apply existing adjustment tools and allow users to evaluate their benefits interactively. We used the BatchQC pipeline on both simulated and real data to demonstrate the effectiveness of this software toolkit.BatchQC is available through Bioconductor: http://bioconductor.org/packages/BatchQC and GitHub: https://github.com/mani2012/BatchQC CONTACT: wej@bu.eduSupplementary information: Supplementary data are available at Bioinformatics online.

Publications

  1. BatchQC: interactive software for evaluating sample and batch effects in genomic data.
    Cite this
    Manimaran S, Selby HM, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Bravo HC, Johnson WE, 2016-12-01 - Bioinformatics (Oxford, England)

Credits

  1. Solaiappan Manimaran
    Developer

    Division of Computational Biomedicine, Boston University School of Medicine, United States of America

  2. Heather Marie Selby
    Developer

    Bioinformatics Program, Boston University, United States of America

  3. Kwame Okrah
    Developer

    gRED Oncology Biostatistics, Genentech

  4. Claire Ruberman
    Developer

    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, United States of America

  5. Jeffrey T Leek
    Developer

    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, United States of America

  6. John Quackenbush
    Developer

    Department of Biostatistics, Harvard T.H. Chan School of Public Health, France

  7. Benjamin Haibe-Kains
    Developer

    Ontario Institute of Cancer Research, Toronto, Canada

  8. Hector Corrada Bravo
    Developer

    Center for Bioinformatics and Computational Biology, University of Maryland, United States of America

  9. W Evan Johnson
    Investigator

    Bioinformatics Program, Boston University, United States of America

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Summary
AccessionBT000040
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByW Evan Johnson