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Affymetrix® Expression Console™ Software  

Affymetrix Expression Console Software supports probe set summarization and CHP file generation for 3' IVT expression arrays, whole-transcriptome arrays, and miRNA arrays.

Download Available below

Affymetrix Expression Console Software

Expression Console Software is an easy-to-use software package openly available to all Affymetrix expression array users. Every researcher now has the ability to normalize, perform data quality control, and summarize data from thousands of samples, tens of thousands of genes, hundreds of thousands of exons, or hundreds of thousands of different transcript isoforms using a standard desktop computer.

Affymetrix, the leader in gene expression over the last 20 years, continually provides investigators with innovative solutions to fit their research needs. Detailed analysis is now at the fingertips of every researcher, regardless of access to bioinformatics resources, through our Affymetrix Expression Console Software and new Affymetrix® Transcriptome Analysis Console (TAC) Software.

Simple and powerful analysis at your fingertips

  • Convenient standardized workflows for both gene-level and exon-level analysis
  • Flags outlier samples based on configurable QC metrics
  • Principle Component Analysis (PCA) using CEL intensities or CHP signal values
  • Seamless integration into TAC Software

The software provides a convenient, easy-to-use analysis workflow that enables CHP files to be generated from CEL files with minimal effort using standardized approaches tailored by Affymetrix. Alternatively, more advanced users can configure the background correction, normalization, and summarization methods to meet the needs of their experimental research.

Data workflow

Video tutorials to help guide you

Affymetrix has created a series of short videos to help guide you through data analysis at your own pace. These videos provide examples of taking array CEL files through gene level and alternative splicing differential expression analysis.

View EC and TAC analysis tutorials

Powerful visualization tools

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, including:

PCA plot and signal histogram for fast and simple identification of outlier samples

Signal scatter plot for visualization of changes between conditions

Pearson correlation plot of signal or detection vs. p-value

Signal box plot visualizes the ratio of individual probe intensity to the median probe intensity across all arrays

Download information and instructions

Download the latest version of Expression Console Software, version 1.4.1 (64-bit. This version is supported by both Windows® 7 (64-bit) and Windows® 8 (64-bit) operating systems. *Posted on 02/13/2015

Expression Console Software is compatible with:

  • GeneChip® Command Console® (AGCC) Software as the primary probe set summarization tool. The integration of Expression Console™ Software 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.
  • NEW Affymetrix Transcriptome Analysis Console Software for visualization of expression changes at the gene and exon levels. The software package also provides the capability of performing alternative splicing analysis with GeneChip® Human Transcriptome Array 2.0.
  • GeneChip-compatible™ Software Solutions catalog for a list to find the appropriate solution for downstream analysis of GeneChip data for your research.

Related Products

Transcriptome Analysis Console (TAC) Software – NEW
Genotyping™ Console Software
GeneChip® Data Transfer Tool (DTT)
GeneChip-compatible™ Software
Affymetrix Tools – developed internally at Affymetrix


For Research Use Only. Not for use in diagnostic procedures.

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