Comments regarding these tools can be submitted to the upcoming 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.

Affymetrix Power Tools (APT) - 10/5/2006

Affymetrix Power Tools contains C++ code for analyzing Affymetrix data and a set of command line tools built on this source code.

seg-limo (SEGmented LInear MOdel) - 12/7/2006

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seg-limo detects regions of differential expression from multiple transcription tiling array data sets at a user specified False Discovery Rate. It outputs the regions together with differential expression estimates in egr format for convenient visualization in the Integrated Genome Browser. It is written in ANSI C++ and has been tested on Intel Linux, both 32 and 64 bit. The source code is being distributed under the GPL license.

Copy Number Pipeline - 3/30/2007

• Copy Number Pipeline Binaries: Linux (32 bit and 64 bit), Windows, Mac (Fat binary: Intel & PPC), and Sparc Sun Solaris. (bz2, 15 MB)
• Library, parameter files, and SNP covariate files for Mapping 500K array. (b2, 69 MB)
• Library and SNP covariate files for Mapping 100K array. (b2, 21 MB)
• Library and SNP covariate files for Mapping 10K array. (b2, 5.7 MB)
• Example input data. (bz2, 755 MB)
• Example output data (created using example command lines included in the README). (bz2, 206 MB)
• Contains all of the above. (bz2, 1.1 GB)

Id_compare - 5/5/2006

Terms and Conditions | Download

This is the command-line application for the Copy Number Pipeline which was developed for doing chromosome copy number and loss of heterozygosity analysis based on Affymetrix Mapping 500K arrays. This can also be used for the 100K and 10K arrays.

Id_compare (version 1.0) is a tool for fast calculation of single-marker and multi-marker SNP correlations on a whole-genome scale. It is ideally suited for determination of genetic coverage for whole genome SNP panels and for generating raw SNP correlation data useful for selection of tag SNPs or evaluation of SNP tagging strategies.

Affymetrix Tools

The Integrated Genome Browser and other tools are available in the Affymetrix Tools web page.

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NetAffx Download Utility

Download | Docs | Terms and Conditions

This utility provides a Windows operating system service to periodically query the NetAffx site and download user specified annotation files when updates are made available. Use the control panel applet that is installed with the software to configure the software. Commercial software providers are required to purchase a NetAffx Use License to bundle NetAffx content in their applications. Use of this software tool does not grant or substitute for this license.

gtype_cel_to_pq

Download | Terms and Conditions

gtype_cel_to_pq tool extracts probesets from genotyping CEL filess into tab-delimited text suitable for import into other tools such as R.

Tiling Utilities

Download | Terms and Conditions

This is a collection of basic command-line utilities useful for working with tiling array data. They are all basic format conversion utilities for moving data between different formats related to tiling arrays, including tab-delimited text.

Expression Intensity Exporter

Download | No Docs Available | Terms and Conditions

This tool will export the PM and MM intensities from an expression array to a text file.

Mapping Intensity Exporter

Download | No Docs Available | Terms and Conditions

This tool will export the PM and MM intensities from a mapping array to a text file.

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Affymetrix Tools

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