Scientific Publications
The list of probe sets for an expression or genotyping probe array can be obtained from either the PSI or CDF file. The probe set name in a genotyping probe array is the SNP name as displayed by Affymetrix software.
The PSI file is a simple ASCII text file with just the probe set names and number of probe pairs per probe set. The CDF file contains the probe set names plus the X/Y coordinates for all probe pairs.
The CDF file comes in an ASCII and binary format. The parsers in the File SDK use memory mapping techniques so random access of binary CDF files is very quick. For the ASCII CDF files, the File SDK reads the entire file into memory.
The most efficient way to obtain the list of probe set names is to read the PSI file. Reading a binary CDF file for the probe set names is also very efficient, but you will need to determine if the file is of the binary format.