Affymetrix® Data File Formats - Introduction

The Affymetrix Data Files include the .EXP, .DAT, .CEL, .CHP, .CNCHP, .LOHCHP, .CNVCHP, .CYCHP, .DMET.CHP, CDF, .BAR, .BPMAP, .TPMAP, .PSI, .MSK, .GRD, and .GRC files generated and managed by Affymetrix® GeneChip® software. This documentation is intended to provide comprehensive technical detail on the format and specifications of these Affymetrix Data Files. Additional support is not provided other than the documentation available in this web page.

Software developers are strongly encouraged to use the Affymetrix Fusion SDK (rather than direct file format compatibility) in accessing the information stored within the data files. The Fusion SDK provides parsing abilities for GCOS 1.x and Command Console files.

We expect changes to be made to the Affymetrix file formats frequently during the foreseeable future as the instrumentation and microarray platform evolves to support higher performance requirements, new applications, and an ever shrinking microarray feature size. Thus, we expect that software built to access the files directly, rather than through the Fusion SDK, may be somewhat less robust during periods of file format evolution.

Having stated the above, Affymetrix does realize that there are occasions when use of the Fusion SDK may not be practical, when unfiltered access to data is required. It is for these circumstances that Affymetrix is making the file format documentation available to you. As with all unfiltered products, please consider your use of direct file format access carefully. We wish you good luck.

Our policy is to support only versions of the file formats which will be or have been commercially released. Beta versions of file formats will not be supported. We will document new or revised formats as soon as commercially feasible. However, please be aware that our own development cycles may not finalize new formats with enough lead time to be allow you to support them at initial release. Use of the documentation provided is offered to those solutions providers who understand and accept these support limitations.

We are pleased to have you working with the Affymetrix platform. Please consider joining the Affymetrix Developers Network distribution list in order to keep up to date with upcoming changes to the platform and the resources to help you leverage them in your work.