title: BatchQC: interactive software for evaluating sample and batch effects in genomic data.
abstract: 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.
authors.affiliation: Department of Biostatistics, Boston University, Boston, MA.|Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA.
authors.forename: Solaiappan
authors.initials: S
authors.lastname: Manimaran
authors.affiliation: Bioinformatics Program, Boston University, Boston, MA.
authors.forename: Heather Marie
authors.initials: HM
authors.lastname: Selby
authors.affiliation: gRED Oncology Biostatistics, Genentech, South San Francisco, CA.
authors.forename: Kwame
authors.initials: K
authors.lastname: Okrah
authors.affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD.
authors.forename: Claire
authors.initials: C
authors.lastname: Ruberman
authors.affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD.
authors.forename: Jeffrey T
authors.initials: JT
authors.lastname: Leek
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA.|Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA.
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
authors.affiliation: Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Ontario, Canada.|Princess Margaret Cancer Centre, University Health NetworkToronto, Ontario, Canada.|Ontario Institute of Cancer Research, Toronto, Ontario, Canada.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Haibe-Kains
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD.
authors.forename: Hector Corrada
authors.initials: HC
authors.lastname: Bravo
authors.affiliation: Department of Biostatistics, Boston University, Boston, MA.|Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA.|Bioinformatics Program, Boston University, Boston, MA.
authors.forename: W Evan
authors.initials: WE
authors.lastname: Johnson
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D012984:Software; D014584:User-Computer Interface