Difference of CN probes and SNP probes on genotyping microchip arrays

Question

[Jimbou]

Is there a difference between copy number (CN) probes compared to SNP probes on SNP arrays such as the Affymetrix 6.0 SNP array? Physically there could be longer oligos for the CN probes? Do you have to analyse both probes differently, e.g. do tools such as PennCNV use both probes for CNV detection?