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GeneChip® Command Console® Software (AGCC)  

GeneChip® Command Console® Software (AGCC) is the latest generation of instrument control software for GeneChip systems.

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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™, Axiom™ Analysis Suite, 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

To obtain the latest version of Command Console Software (AGCC), please select the link below.

Command Console Software 4.1.2 (zip, 383 MB) * Posted on 07/07/14

AGCC 4.1.2 has been validated on Windows XP 32Bit and Windows 7 64Bit. Customers who currently have a 32-bit instrument workstation may need to either purchase a new 64-bit workstation or upgrade their workstation to 64-bit via an Affymetrix-recommended upgrade path. All customers seeking to upgrade to Windows 7 64Bit are requested to kindly consult with Affymetrix support (888-DNA-Chip) to discuss compatibility and upgrade paths and get the necessary support. Failure to do so may lead to system incompatibilities.

The Array Traceability Viewer (ATV ) software is installed on GeneTitan MC instrument control workstations where Affymetrix GeneChip Command Console (AGCC) is installed . The software offers the capability to (i) View the processing status for plates run on a particular instrument. (ii) View the sample and processing status for all the arrays on any particular array plate (iii) (iii) Identify the plate where your sample resides. (iv) View and export the sample and experiment attributes at an individual array level.

Array Traceability Viewer (zip, 101 MB) Posted on 09/25/14


  • 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
Axiom™ Analysis Suite

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

Notification for GeneChip Operating Software (GCOS) and GeneChip Operating Server Software (GCOS Server)

On April 5, 2010, Affymetrix ended support for all versions of GeneChip Operating Software, including GeneChip Operating Server Software referred to as GCOS and GCOS Server, respectively. The GCOS instrument control and data acquisition system have been replaced by the new GeneChip® Command Console® Software (AGCC). Affymetrix software support engineers will no longer provide support for GCOS servers or clients. Affymetrix encourages you to upgrade your software to the latest version of Command Console Software, which can be downloaded above.

To help with migration, Affymetrix has released the GCOS Experiment Export application, which will allow your site to make a copy of all the experiment instance data out of the GCOS database into flat files. The application leaves intact the DAT, CEL, and CHP files in the GCOS data directory associated with GCOS experiments. The Data Exchange Console application installed by Command Console Software can be used to convert the experiment data into flat files, and DAT and CEL files into the GeneChip Command Console format flat files, at your convenience. The GCOS experiment export application eliminates the need to purchase additional storage to convert the GCOS data into Command Console format. Affymetrix software support engineers will support this application at no charge for six months, after which standard support rates will apply. For additional information on the GCOS Experiment Export application, please contact any one of our software support engineers.


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