Once the gesnp.cpp and random.cpp code is downloaded to a UNIX box, 
compile the code using the following command from the working directory:

g++ gesnp.cpp -o gesnp

The code is now compiled.

Library and CEL files must be scrubbed before being used in the program.

To scrub a library file, place the proper .CDF file (obtained from Affymetrix) 
in the working directory. Make sure you have execution rights on libScript:

chmod a+x libScript

Name the library file lib.txt and at the command promp type:

./libScript

After the scrubbing a new file in the working directory will be called libNEW.txt.
Remove the old lib.txt and rename libNEW.txt as lib.txt

To scrub a CEL file, place the CEL file in the working directory, at the command promp type:

./celscript CurrentCelFileName.CEL NewCelFileName.CEL

The code is compiled, the library file is scrubbed and all CEL files have been scrubbed.
To call the program at the command line type:

./gesnp #file in group 1 then list files in group 1 and then list files in group 2 > output.txt

So a comparison between 4 files in group 1 and 5 files in group 2 would be:

./gesnp 4 g1_1.cel g1_2.cel g1_3.cel g1_4.cel g2_1.cel g2_2.cel g2_3.cel g2_4.cel g2_5.cel > output.txt

File list that are very long can be written up in a command file and executed from the command file.
