GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor
4179 Microarray technology has become a standard molecular biology tool. experimental data have been generated on a huge number of organisms, tissue types, treatment conditions, and disease states. The Gene expression Omnibus (GEO), hosted by the National Center for Bioinformatics (NCBI) at the National Institutes of Health is a repository of such gene expression measurements. GEO houses information generated from approximately 2580 different experimental series (hundreds comprising cancer datasets) contained in over 57,000 separate samples. Over 1800 different platforms are represented. The BioConductor project is an open-source and open-development software project for the analysis and comprehension of genomic data. The tools contained in the BioConductor project represent many of the most state-of-the-art methods for the analysis of microarray and genomics data. We have developed a set of software tools that allow access to the wealth of information within GEO directly from BioConductor, eliminating many the formatting and parsing problems that have made such analyses problematic in the past. The software, called GEOquery, effectively establishes a bridge between GEO and bioconductor. We discuss the design and use of GEOquery and give examples of the kind of analyses that are facilitated by the software. Easy access to GEO from the BioConductor environment will likely lead to analyses of GEO data using novel and rigorous statistical and bioinformatic tools. Facilitating analyses and meta-analyses of microarray data will increase the efficiency with which biologically important conclusions can be drawn from genomic data.