• Upon the completion of the microarray scan, customers will receive raw scan files on DVDs. These files include: CEL file (cell intensity), .DAT file (raw image), and ARR file (sample information).
  
  
• Affymetrix provides a free software- Transcriptome Analysis Console, which analyzes most gene expression and alternative splicing arrays. This software must be downloaded on a 64-bit PC.
  
  
• Affymetrix Software User Manuals
  

1. Download the Affymetrix Expression Console Software (64-bit version), using this link, http://www.affymetrix.com/estore/browse/products.jsp?productId=131414#1_1
2. Import the CEL files and run appropriate analysis, depending on your array type.
3. From the Tools option in the upper menu, open Transcriptome Analysis Console
4. Import the CHP files that were created via the initial analysis in Gene Expression Console.
5. Run Gene Level, Exon Level, or Alternative Splicing analysis, depending on your  array type.

Other software options:
Partek (accessible through CMGM)
GeneSifter
GeneSpring (accessible through CMGM)