What analysis software packages are available for Exon Array data analysis?
Affymetrix GeneChip Command Console (AGCC) is provided to control the fluidics station, 7G Scanner and generate .dat and .cel files. Probe level analysis of the .cel files is carried out by Expression Console. This software allows for the generation of signal estimates and detection p-values at the probe set level for either exon-level or gene-level analysis. Expression Console Software is freely downloadable from the Affymetrix web site and supported by the Technical Support team. For additional higher levels of analysis, such as alternative splicing detection, a few experimental algorithms are published as methods in respective white papers. Users will need to implement these methods in advanced statistical analysis software packages. These methods have been developed based on experience with limited sample data sets, and further fine-tuning may be required depending on the user’s unique biological systems. It is anticipated that new methods will continue to emerge to better support
