When I loaded the exon array design information and array data into IGB, it seems that the probes were selected from outside of the RefSeq exons. Why?
The most likely explanation is that a different version of the genome assembly has been used to display the array design information and the array results. At launch, two versions of the library files are provided for array analysis corresponding to the Human Genome Build 34 and 35. Take care to use a consistent version number to match the array design with the actual array data for visualization in IGB.