Wikiomics:Exon microarrays

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Technology overview

Overview of the GeneChip® Exon and Gene Array Systems:

Affymetrix White Papers:

  1. Alternative Transcript Analysis Methods for Exon Arrays v1.1 (pdf, 79 KB)]: [1]
  2. Exon Array Background Correction v1.0 (pdf, 78 KB): [2]
  3. Exon Probeset Annotations and Transcript Cluster Groupings v1.0 (pdf, 87 KB): [3]
  4. Exon Related Changes FAQ (pdf, 268 KB):[4]
  5. Gene Level Summarization on Exon Arrays (pdf, 747 KB):[5]
  6. Gene Signal Estimates from Exon Arrays v1.0 (pdf, 428 KB): [6]
  7. Quality Assessment of Exon and Gene Arrays (pdf, 180 KB):[7]

Web-based seminars, including several archived events specific for the Exon arrays can be found at:


Quality control

Affymetrix Whitepaper on exon array QA:

A Core Lab Case Study: Exon Array Challenges and Opportunities:

Array normalization

Data analysis

Exonmap is a BioConductor package, currently under development, that uses the underlying data from X:MAP to support fine grained analysis of Exon array data.

Gene level analysis

Analysis procedure is similar to traditional gene expression arrays, i.e. summarize signals of a probe set (probes mapping to the same gene) into a whole-gene expression index [8].

Exon level analysis

Gene annotation

Analysis tools

Affymetrix support pages for the human, mouse and rat Exon arrays provide library files, annotation files and demonstration data:

The Affymetrix Expression Console is avaialble to download at:

This page also includes a link to Affymetrix Power Tools (APT), which provides additional functionality.

Information about GeneChip compatible 3rd party software for the various applications is available at:

exonmap - BioConductor package to analyse Exon arrays:

dChip - Exon and tiling array analysis:

Data visualization

X:MAP - is an interactive, real-time scrollable, genome browser that shows the location of individual exon probes with respect to their target genes, transcripts and exons.