Affymetrix - Affymetrix Tools - Unsupported tools developed internally at Affymetrix

The tools listed below are all tools that have been developed internally at Affymetrix. They are not validated products and are provided as is and without warranty. Use of these tools is offered to those customers who understand and accept these terms and conditions and wish to take advantage of their potential to help manage and analyze GeneChip data. If any of these tools are to be used in a production environment it is the responsibility of the end-user to perform the required validation.

Comments regarding these tools can be submitted to the Affymetrix forums. Whenever possible, documentation is also provided to help provide guidance on use of the tools. These are the only two methods of help that are provided for these tools.

		DNA AND EXPRESSION TOOLS

		Expression Console™ Download Affymetrix Expression Console software supports Probe Set summarization and CHP file generation for both 3' Expression (e.g. GeneChip® Human Genome U133 Plus 2.0 Array) and Exon Arrays (e.g. GeneChip Human Exon 1.0 ST Array). The Expression Console workflow provides the user with a choice of the more commonly used Probe Set summarization algorithms.

		Genotyping Console™ Download Affymetrix Genotyping Console is a new genotyping analysis software package designed to streamline whole-genome genotyping analysis and quality control for the Genome-Wide SNP Arrays 5.0 and 6.0. Genotyping Console’s QC and visualization tools easily identify and segregate sample outliers. SNP cluster visualization provides a detailed look at the performance of SNPs of interest. Reporting of seventy-two signature SNPs enable verification of a sample’s identity if compared to known genotypes for that sample. In addition, flexible SNP filtering, data management and visualization export features make it easy to share data with collaborators and downstream application software.

		Tiling Analysis Software (TAS) Download The TAS software provides analysis capabilities specifically for the GeneChip Tiling Arrays. TAS analyzes feature intensity data stored in GCOS output .CEL files and produces: Signal and p-values for each genomic position interrogated. Computation of genomic intervals based on computed signal and p-values. Computation of summary statistics Visualizations for assessing the quality of the array data.

		GENOMIC VISUALIZATION TOOLS

		Integrated Genome Browser Download or Launch \| Docs \| IGB Forum \| Terms and Conditions The Integrated Genome Browser (IGB, pronounced ig-bee) is an application intended for visualization and exploration of genomes and corresponding annotations from multiple data sources. Source code for IGB is released under the Common Public License, v1.0, an OSI approved open source license. IGB uses other open source software packages that are distributed in binary form with the IGB source code release, including Xerces from Apache, and Jetty from Mortbay Consulting, which are covered by their own open source licenses. IGB is Copyright (c) 2000-2006 Affymetrix, Inc. Research and development of IGB is supported in part by NIH grant R01HG003040. Source Code

		LIBRARY FILE INSTALLER UPGRADE

		Library File Installer Upgrade Download \| Install Guide The Library File Installer Upgrade is an application to update the CustomExpress™ Arrays expression library files to the latest version. This latest version is required to perform a fresh install of the CustomExpress Arrays expression library files on a GCOS v1.4 Server based on Oracle 10g. This tool requires Java to be installed. Please go to the Java website and download the appropriate Java Runtime Environment. For more information on installation and a quick start guide, please refer to the Install Guide.

		DEVNET TOOLS

		File manipulation and other developer tools are available in the DevNet Tools web page.