An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data
1 Bioinformatics Group, Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Wilmslow Road, Manchester M20 4BX, UK
2 Molecular Biology Core Facility, Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Wilmslow Road, Manchester M20 4BX, UK
Citation and License
Genome Biology 2007, 8:R79 doi:10.1186/gb-2007-8-5-r79Published: 11 May 2007
Affymetrix exon arrays contain probesets intended to target every known and predicted exon in the entire genome, posing significant challenges for high-throughput genome-wide data analysis. X:MAP http://xmap.picr.man.ac.uk webcite, an annotation database, and exonmap http://www.bioconductor.org/packages/2.0/bioc/html/exonmap.html webcite, a BioConductor/R package, are designed to support fine-grained analysis of exon array data. The system supports the application of standard statistical techniques, prior to the use of genome scale annotation to provide gene-, transcript- and exon-level summaries and visualization tools.