Vol. 23 no. 14 2007; pages 1846–1847 | Sean Davis* and Paul S. Meltzer
The article introduces GEOquery, a software tool developed by Sean Davis and Paul S. Meltzer that facilitates access to the Gene Expression Omnibus (GEO) database from the BioConductor project. GEO is a repository of nearly 140,000 gene expression experiments, while BioConductor is an open-source software project for genomic data analysis. GEOquery simplifies the process of downloading and parsing GEO data, making it easier to integrate and analyze these data using BioConductor's advanced methods. The tool supports various GEO entities, including samples, platforms, series, and datasets, and provides custom data structures and methods to organize and manipulate the data. Additionally, GEOquery includes functions to convert GEO data into BioConductor's MAList and ExpressionSet data structures, enabling seamless integration with existing BioConductor workflows. The authors highlight the potential of GEOquery to enhance the efficiency and accessibility of microarray data analysis, particularly for meta-analyses and novel statistical and bioinformatic tools.The article introduces GEOquery, a software tool developed by Sean Davis and Paul S. Meltzer that facilitates access to the Gene Expression Omnibus (GEO) database from the BioConductor project. GEO is a repository of nearly 140,000 gene expression experiments, while BioConductor is an open-source software project for genomic data analysis. GEOquery simplifies the process of downloading and parsing GEO data, making it easier to integrate and analyze these data using BioConductor's advanced methods. The tool supports various GEO entities, including samples, platforms, series, and datasets, and provides custom data structures and methods to organize and manipulate the data. Additionally, GEOquery includes functions to convert GEO data into BioConductor's MAList and ExpressionSet data structures, enabling seamless integration with existing BioConductor workflows. The authors highlight the potential of GEOquery to enhance the efficiency and accessibility of microarray data analysis, particularly for meta-analyses and novel statistical and bioinformatic tools.