Scientific Publications
DevNet Tools
The tools listed below are all unsupported 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 the associated 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 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) - 10/23/2009
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
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)
ld_compare - 5/5/2006
Terms and Conditions | Download
ld_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.
miRNA QC Tool - 11/10/2009
Download | Terms and Conditions
An updated version of the miRNA QC tool, version 1.0.33.0, is now available.
The miRNA QCtool is a free, unsupported software tool from Affymetrix. It enables a variety of analysis methods tailored to miRNA studies and features extensive quality control tools. Several methods of probe signal background subtraction, array normalization (including the use of internal normalization controls), and probe set summarization are allowed, in various combinations. If you are using internal normalization controls, you can apply the default probe sets (human 5.8S rRNA) or choose from any set of the probe sets on the array, including snoRNAs, miRNAs (any species), or spike-in controls. The miRNA QCtool is thus applicable to a wide variety of experimental designs.
Affymetrix Tools
The Integrated Genome Browser and other tools are available in the Affymetrix Tools web page.
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.
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.
Affymetrix Tools
File manipulation and other developer tools are available in the Affymetrix Tools web page.