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Affymetrix® GeneChip® Command Console® Software (AGCC)

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Affymetrix® GeneChip® Command Console® Software (AGCC) is the latest generation of instrument control software for GeneChip systems. Command Console Software provides an intuitive set of tools for instrument control and data management used in the processing of GeneChip Arrays. The software summarizes probe cell intensity data (CEL file generation) and enables sample and array registration, data management, instrument control as well as automatic and manual image gridding. Besides these core features, the flexible platform provided by Command Console Software enables customized, automated, and integrated workflows with a variety of laboratory information management systems. Probe-level summarization (CHP) files are generated by other Affymetrix software applications.

Command Console Software supports the full range of Affymetrix assays by enabling seamless integration with downstream primary analysis applications such as Affymetrix Expression Console™ and Genotyping Console™. Sample attribute and array data can be directly imported into any of the more than 30 commercially available GeneChip-compatible™ applications, allowing researchers and clinicians to select from a variety of analysis methodologies. Key to this ability is Affymetrix' commitment to an open informatics platform that uses industry-standard file formats for sample annotations and open file formats to access GeneChip Array data. Inside GeneChip-compatible analysis applications, sample attributes and array data are merged with automated downloads of library files and NetAffx® annotations, providing streamlined data analysis workflows unmatched by any other microarray platform.

Download Information and Instructions

Command Console Software 3.0.1 (zip, 407 MB)  * Posted on 11/03/09

Command Console Software 2.0.1 (zip, 231 MB)  * Posted on 03/16/09

Command Console Installation Instructions 3.0.1 (pdf, 3.38 MB)


  • File-based software for easy data sharing
  • Flexible GeneChip processing workflow
  • Integrated instrument control
  • Simplified data management
  • Integration and customization for end users and third-party software tools

Instrument Support

This release of Command Console Software supports the following instruments:

  • GeneTitan™ Instrument
  • Fluidics Station 450
  • GeneChip® Scanner 3000
  • All research-use-only models are supported. The GeneChip® Scanner 3000 Dx is not supported.

Array Support

This release of Command Console Software supports all cartridge-based arrays and array plates.

Additional Information

  • Affymetrix Developers' Network web pages contain archived web talks on the Command Console technology, as well as information on the Fusion SDK (compatible with both GCOS and Command Console Software), including source code. Software developers: learn more about integrating with Command Console Software.
  • Command Console Software User Documentation
  • Introduction to Command Console Software in the Training & Tutorials section

Related Products

Affymetrix® Genotyping Console™ Software
Affymetrix® Expression Console™ Software
Affymetrix Software Products
GeneChip-compatible™ Software
Affymetrix Tools - Developed internally at Affymetrix

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