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Affymetrix^® GeneChip^® Command Console^® Software (AGCC)

Overview

Literature

Tools & Data

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Affymetrix® GeneChip® Command Console® Software (AGCC) is the latest generation of instrument control software for GeneChip systems. AGCC provides an intuitive set of tools for instrument control and data management used in the processing of GeneChip probe arrays. AGCC summarizes probe cell intensity data (.CEL file generation) and enables sample and array registration, data management, fluidics and scanning instrument control as well as automatic and manual image gridding. Besides these core features, the flexible platform provided by AGCC 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.

AGCC 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 microarray 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 (zip, 166 MB) * Posted on 05/15/08
Command Console Installation Instructions (pdf, 3.2 MB)

Benefits

Easily share data from this file-based software
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 AGCC supports the following instruments:

Fluidics Station 450
GeneChip Scanner 3000
All research use models are supported. GCS3000 Dx is not supported

Array Support

This release of AGCC supports all cartridge-based arrays.

HT plates will be supported in a future release of AGCC

Additional Information

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