Affymetrix Expression Console Software (v.1.0)

Category Genomics>Gene Expression Analysis/Profiling/Tools

Abstract The Affymetrix Expression Console Software provides signal estimation and Quality Control (QC) functionality for the GeneChip Expression Arrays (3 Expression Arrays and Exon Arrays). It provides the ability to create summarized expression values (CHP files) for individual or collections of 3' Expression Array and Exon Array feature cell intensity (CEL) files.

Note 1: The CHP file contains the analysis results from a Microarray Suite analysis (expression, CustomSeq, Genotyping...). The CEL (cell intensity) file contains only intensity information for a given probe on an array.

In addition to CHP writing, the Expression Console Software also produces a collection of QC metrics for evaluating the success of hybridizations. The user defines thresholds for these metrics and the software highlights the metrics that do Not meet the defined thresholds. In addition, the CHP files are highlighted in the study table portion of the software, if they have any metrics outside of the defined thresholds.

The Expression Console application contains graphic capabilities for visual inspection of the hybridization results.

To identify outliers, the application is designed to display:

1) Line graphs for individual or collections of metrics or probe sets

2) Box plots for signal distributions before or after normalization

3) MvA plots for signal distributions

4) Heat maps for correlation matrices

The Affymetrix Expression Console Software is targeted for research personnel (such as laboratory technicians, research associates, and scientists) analyzing Affymetrix GeneChip data.

Note 2: The Expression Console application is Not a secondary gene expression analysis package. However, it does create the CHP files required for secondary gene expression analysis package(s) that can be selected from the Affymetrix GeneChip Compatible Program and/or other third party gene expression analysis packages.

Note 3: See G6G Abstract Number 20072 for additional product info from this manufacturer.

System Requirements

Microsoft Windows 2000 Professional with service pack 4.0 or Higher; Microsoft Windows XP with service pack 2.0 or higher. The minimum hardware recommendations are: Memory (RAM): 1 GB*, Hard drive: 20 GB** (sufficient space should be available to meet user data requirements); Processor: 2.0 GHz Intel Pentium or higher.

*Due to the large number of datapoints produced by the Exon Arrays, an additional 1GB of RAM is highly recommended.

**The larger file sizes associated with Exon Array data should be taken into account when calculating the necessary free space requirement.


Manufacturer Web Site Affymetrix, Inc.

Price Contact manufacturer.

G6G Abstract Number 20001

G6G Manufacturer Number 100120