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.

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 softwares 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.