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.

Download information and instructions

To obtain the latest version of Command Console Software (AGCC), please select the AGCC 4.3.2 Upgrade link below. AGCC 4.3.2 is a software upgrade and should be installed on AGCC 4.1.2

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.

 GeneChip Command Console Software 4.3.2 Upgrade Only (zip, 63 MB)

AGCC 4.3.2 is a software upgrade that can only be used to upgrade AGCC GeneTitan Instrument Control workstations that have AGCC 4.0 or above already installed. The package includes all software updates that followed the 4.0 release, so any of these versions can be directly updated to 4.3.2. Please refer to the release notes in the AGCC 4.3.2 installation package for a full description of the changes in AGCC 4.3.2. Please note AGCC 4.3.2 is not a full installation package.

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.

 GeneChip Command Console Software 4.3.3 Patch Only (exe, 31.3 MB)

AGCC 4.3.3 is a software patch to address the issue of batch registration errors once Microsoft Security Update KB4041681 is applied. The patch requires existing installation of AGCC 4.1.2 for GCS3000 or 4.3.2 for GeneTitan instrumentation. It is recommended for all Windows 7 users running AGCC 4.1.2 or higher.

Refer to the AGCC 4.3.3 release notes for more information prior to installation of this patch.

 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.
  • Introduction to Command Console Software in the Training & Tutorials section