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Related Experiment Videos

beadarray: R classes and methods for Illumina bead-based data.

Mark J Dunning1, Mike L Smith, Matthew E Ritchie

  • 1Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK. md392@cam.ac.uk

Bioinformatics (Oxford, England)
|June 26, 2007
PubMed
Summary
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The beadarray R/Bioconductor package simplifies processing of raw Illumina data. It offers flexible analysis options and quality assessment for downstream bioinformatics tasks.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Illumina bead arrays are widely used for high-throughput genomic experiments.
  • Proprietary software often limits flexibility in data analysis.
  • Standardized data formats are crucial for reproducible research.

Purpose of the Study:

  • To introduce the beadarray R/Bioconductor package for handling Illumina raw data.
  • To provide users with flexible options for image processing, background correction, and normalization.
  • To enable quality assessment and data summarization for downstream analyses.

Main Methods:

  • The beadarray package facilitates reading and storing raw Illumina data in R classes.
  • It allows users to select from various image processing, background correction, and normalization methods.

Related Experiment Videos

  • The package supports quality assessment of raw data and summarization for other R/Bioconductor packages.

    • Main Results:

    • The beadarray package enables flexible and customizable analysis of Illumina data.
    • It allows for quality assessment directly on raw experimental data.
    • Users can integrate beadarray processed data with other R/Bioconductor tools for further analysis.

    Conclusions:

    • The beadarray package enhances the analysis of Illumina high-throughput data by offering flexibility and control.
    • It promotes reproducible research by providing standardized data handling and analysis options.
    • The package is a valuable tool for researchers in genomics and bioinformatics.