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.


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.


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.


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


For Research Use Only. Not for use in diagnostic procedures.