The Affymetrix™ Developers Network provides a collection of technical information and tools to assist software developers in their development, testing and validation efforts.

DevNet tools

Affymetrix DevNet Tools are all unsupported tools that have been developed internally at Thermo Fisher Scientific. They are not validated products and are provided as is and without warranty.

Array data

At the heart of Affymetrix Informatics is the data generated from a microarray. Thermo Fisher Scientific provides a variety of open solutions to gain access to these data from file format documentation to open source code.

File formats

Fusion SDK

The Fusion SDK is a combination of the existing ANSI C++ GCOS 1.x File SDK and Command Console File SDK. Fusion will provide backwards and forward flexibility by providing the ability to parse GCOS 1.x and Command Console files.

Data resource center (sample data & data sets)

A comprehensive collection of Affymetrix sample data and data sets that will aid in your software development efforts.

Annotations

Data from Affymetrix tools is only as powerful as one's ability to intersect them with the genomic information represented on the array. The Affymetrix NetAffx™ site offers a web-based user-interface to retrieve these annotation information. These same annotation information can be incorporated within a software application through the use of the NetAffx SDK.

NetAffx SDK

The NetAffx SDK is a set of Application Programming Interfaces (APIs) used to download the annotations available on the NetAffx web site. The NetAffx SDK can also be used to automate the download of library files within an application.

NetAffx SDK webcast

This WebTalk presents an overview of the NetAffx Software Developers Kit and how it can be used to automate the retrieval of NetAffx annotation files.

NetAffx SDK—exon expression analysis

View a table of all available resources hosted through the NetAffx SDK for the analysis of exon expression arrays.

Deep linking to probe set information

Review the NetAffx deep link manual to learn how to link directly to NetAffx probe set summaries from within your own applications or web sites using a convenient deep link URL.

Attributes

Analysis of Affymetrix microarrays often is focused on comparing samples that have different attributes. Affymetrix core software like GCOS and GeneChip Command Console allow users to input sample attributes into the system and associate these attributes with the array data through simple XML files. The associated DTD files will aid software developers in gaining access to this information and maintaining it with its associated microarray data.

"Command Console" array sample attribute file DTD (April, 2006)

Sample attributes in Command Console are stored in *.ARR files. This is the DTD for the ARR files.

Analysis

Following the scanning of an array, a DAT file is created. Then a grid is applied onto this file creating a CEL file. The following collection of tools focuses on the data summarization process to generate the downstream CHP file that is created after the CEL file is generated.

Affymetrix Power Tools

The Affymetrix Power Tools (APT) are a set of command-line tools that implement several key algorithms of interest around the GeneChip platform including BRLMM, PLIER, RMA, DABG and MASv5.

MAS5 Stat SDK

The MAS5 Stat SDK provides source code for the implementation of the MAS5 Expression Statistical Algorithm.