Showing papers by "Robert Gentleman published in 2003"
TL;DR: Three of the most widely used and comprehensive statistical analysis tools written in R through the Bioconductor project are reviewed, the Java-based TM4 software system available from The Institute for Genomic Research, and BASE, the Web-based system developed at Lund University.
Abstract: DNA microarray assays represent the first widely used application that attempts to build upon the information provided by genome projects in the study of biological questions. One of the greatest challenges with working with microarrays is collecting, managing, and analyzing data. Although several commercial and noncommercial solutions exist, there is a growing body of freely available, open source software that allows users to analyze data using a host of existing techniques and to develop their own and integrate them within the system. Here we review three of the most widely used and comprehensive systems, the statistical analysis tools written in R through the Bioconductor project (http://www.bioconductor.org), the Java-based TM4 software system available from The Institute for Genomic Research (http://www.tigr.org/software), and BASE, the Web-based system developed at Lund University (http://base.thep.lu.se).
295 citations
TL;DR: The system currently provides parsers to process annotation data from LocusLink, Gene Ontology Consortium, and Human Gene Project and can be extended to new data sources via user defined parsers.
Abstract: SUMMARY AnnBuilder is an R package for assembling genomic annotation data. The system currently provides parsers to process annotation data from LocusLink, Gene Ontology Consortium, and Human Gene Project and can be extended to new data sources via user defined parsers. AnnBuilder differs from other existing systems in that it provides users with unlimited ability to assemble data from user selected sources. The products of AnnBuilder are files in XML format that can be easily used by different systems. AVAILABILITY (http://www.bioconductor.org). Open source.
61 citations
TL;DR: The results identify novel components of the graft response to transplantation injury and rejection that are identified in genes classified as defense, communication, and metabolism.
Abstract: Little is known regarding the graft response to transplantation injury. This study investigates the posttransplantation response of genes that are constitutively expressed in the heart. Constitutiv...
15 citations
01 Jan 2003
TL;DR: A framework for reducing and interpreting results of multiple microarray experiments and a flexible genefiltering procedure, a dynamic and extensible annotation system, and methods for visualization are provided.
Abstract: We provide a framework for reducing and interpreting results of multiple microarray experiments. The basic tools are a flexible genefiltering procedure, a dynamic and extensible annotation system, and methods for visualization. The gene-filtering procedure efficiently evaluates families of deterministic or statistical predicates on collections of expression measurements. The expression-filtering predicates may involve reference to arbitrarily complex predicates on phenotype or genotype data. The annotation system collects mappings between manufacturer-specified probe set identifiers and public use nomenclature, ontology, and bibliographic systems. Visualization tools allow the exploration of the experimental data with respect to genomic quantities such as chromosomal location or functional groupings.
14 citations