Contains functions for the storage, management and analysis of oligonucleotide arrays. affy provides the user with extreme flexibility when carrying out an analysis and make it possible to access and manipulate probe intensity data. The affy package was designed to balance user control of data analysis with convenience. Graphical user interfaces, object oriented programming and modular function design enhance the convenience of the package.
A package that provides a report with diagnostic plots for one or two colour microarray data. After preparation of the data, a single command line is used to create the report. The quality metrics assess reproducibility, identify apparent outlier arrays and compute measures of signal-to-noise ratio. arrayQualityMetrics handles most current microarray technologies and is amenable to use in automated analysis pipelines or for automatic report generation, as well as for use by individuals. Its main benefits are its simplicity of use, the ability to have the same report for different types of platforms, and the opportunity for users or developers to extend it for their needs. arrayQualityMetrics can be used for individual data analyses or in routine data production pipelines, to provide fast uniform reporting. The diagnosis of quality remains, in principle, a context-dependent judgement, but this tool provides powerful, automated, objective and comprehensive instruments on which to base a decision.
A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models.
Scans and processes up automatically to 100 microarray raw image files. Agilent's Feature Extraction is a software that locates and places microarray grids, rejects aberrant pixels, accurately determines intensities and characteristic ratios, marks aberrant pixels and calculates statistical confidences. This commercial application is compatible with some non-Agilent scanners. In this software, application-specific QC reports provide metrics targeted to the experiment.
Provides access to a variety of QC metrics for assessing the quality of RNA samples and of the intermediate stages of sample preparation and hybridization. Simpleaffy also offers fast implementations of popular algorithms for generating expression summaries and detection calls. It is designed to work alongside the core ‘affy’ package from BioConductor and provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like.
Offers a platform for producing Robust Multiarray Average (RMA) expression values from Affymetrix files. RMAExpress includes features for reading raw files, determining RMA expression values and to perform a quality check. The application also includes two additional modules: (i) RMADataConv that allows the conversion of CDF and CEL files and; (iii) RMAExpressConsole that gives access to a command-line interface for extracting RMA expression values from a set of CEL files. The software is part of the Affy package.