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) - 4/21/2015
Affymetrix Power Tools contains C++ code for analyzing Affymetrix data and a set of command line tools built on this source code.
SNPolisher is an R package for post-process analyses of Affymetrix' Axiom® genotyping array results. SNPolisher calculates QC metrics for each SNP; classifies SNPs into categories; generates cluster plots for each SNP to evaluate quality; genotypes OTV SNPs to produce AA, AB, BB, and OTV clusters; changes SNP calls during post-processing; tests for intensity shifts between batches; reformats Axiom® output for use with fitTetra; and reformats fitTetra output for classification and visualization in SNPolisher. The input files are the standard output files from Axiom® arrays.
Both R and perl (64-bit) must be installed for SNPolisher to run. To install SNPolisher, download the zipped package file. This folder contains the SNPolisher R package file, the User's Guide, the Quick Reference Card, and several example data sets. Unzip the folder, and then install the R package (SNPolisher_1.5.2.tar.gz). Follow the detailed instructions in the User Guide to install perl, R, and the SNPolisher package.
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
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.
The Integrated Genome Browser and other tools are available in the Affymetrix Tools web page.
NetAffx Download Utility
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.
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.
File manipulation and other developer tools are available in the Affymetrix Tools web page.