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Open source software for the analysis of microarray data.

Sandrine Dudoit1, Robert C Gentleman, John Quackenbush

  • 1University of California, Berkeley, CA, USA.

Biotechniques
|April 1, 2003
PubMed
Summary
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This review covers three open-source software systems—Bioconductor, TM4, and BASE—for managing and analyzing DNA microarray data, addressing a key challenge in biological research.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • DNA microarrays are crucial tools for biological research, leveraging genome project data.
  • Effective data management and analysis are significant challenges in microarray studies.

Purpose of the Study:

  • To review and compare three prominent open-source software systems for DNA microarray data analysis.
  • To highlight solutions for data collection, management, and analysis in biological research.

Main Methods:

  • Review of Bioconductor (R-based statistical tools).
  • Evaluation of TM4 (Java-based software system from TIGR).
  • Assessment of BASE (Web-based system from Lund University).

Main Results:

Related Experiment Videos

  • These systems offer freely available solutions for complex microarray data analysis.
  • They support existing techniques and allow for the development and integration of new methods.

Conclusions:

  • Open-source software provides powerful and accessible tools for advancing DNA microarray research.
  • Bioconductor, TM4, and BASE are leading systems enabling comprehensive data analysis in genomics.