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Affymetrix® Expression Console™ Software

Affymetrix® Expression Console™ Software

Tables and graphs in PDF format
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Tables and graphs in PDF format
Tables and graphs in PDF format
3' IVT Expression Array Report Controls window
3' IVT Expression Array Report Controls window
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3' IVT Expression Array Report Controls window
3' IVT Expression Array Report Controls window
Export Probe Set Results (pivot table) to TXT
Export Probe Set Results (pivot table) to TXT
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Export Probe Set Results (pivot table) to TXT
Export Probe Set Results (pivot table) to TXT

Expression Console™ software supports probe set summarization and CHP file generation for 3' expression (e.g., GeneChip® Human Genome U133 Plus 2.0 Array), gene-level (e.g., GeneChip® Human Gene 1.0 ST array) and exon-level arrays (e.g., GeneChip® Human Exon 1.0 ST Array). The Expression Console workflow provides the user with a choice of the more commonly used probe set summarization algorithms. The algorithms offered include:

  • MAS5 Statistical algorithm
  • Probe Logarithmic Intensity Error Estimation (PLIER)
  • Robust Multichip Analysis (RMA)

Additionally, GeneChip data quality control is a key component to this workflow and is augmented by a variety of visualization and graphing tools provided by Expression Console™ software.

Affymetrix GeneChip-compitable software

For new users or those looking for convenience, the software provides an easy-to-use analysis workflow that enables CHP files to be generated from CEL files with minimal effort using a standardized approach specifically tailored by Affymetrix for each array type. Alternatively, more advanced users can configure the background correction, normalization and summarization methods to meet the needs of their experimental research.

Download information and instructions

Download Expression Console™ Software (zip, 40 MB) * Posted on 10/24/07

Download Expression Console™ Release Notes (pdf, 40 KB)

Expression Console™ software is compatible with:

  • GeneChip® Command Console® (AGCC) software as the primary probe set summarization tool. The integration of Expression Console™ and the AGCC software enables sample attribute information collected in the AGCC interface to be viewed in the Expression Console study window and used to guide the user's analysis and QC interpretations.
  • GeneChip® Operating Software (GCOS) as an alternative probe set summarization choice, providing the user with a wider variety of new analysis and QC tools not currently available in GCOS. (Please note, CHP files created in Expression Console using either the PLIER or RMA summarization algorithms are not supported by the GCOS database).


It is important to note that Affymetrix® Expression Console™ software is not intended to replace secondary analysis packages for the statistical filtering of expression results and the creation of gene lists. Please refer to the GeneChip-compatible™ Software Solutions catalog for a list to find the appropriate solution for downstream analysis of GeneChip data for your research.

Benefits

  • Supports both GCOS and AGCC CEL file outputs
  • Integrated with the AGCC file-based data structure
  • Standardized workflows for those looking for convenience for both gene-level and exon-level analysis
  • Expanded gene-level configuration choices allowing experienced users to tailor analyses
  • Selection of QC tools for evaluating the success of individual hybridizations
  • Flagging of outlier samples based on user configurable QC metrics
  • Simplified GUI for exon analysis
  • Performance improvements over ExACT resulting in substantially reduced analysis time requirements

Additional Information

For users of ExACT, Affymetrix® Expression Console™ will be replacing this application.
Expanded functionality is available in the Affymetrix Power Tools (APT).

Related Products

GeneChip® Operating Software
Genotyping Console Software
GeneChip® Data Transfer Tool (DTT)
GeneChip-compatible™ Software
Affymetrix Tools - Developed internally at Affymetrix

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