Before you can process CEL files with SCAN, you need to complete the preliminary steps outlined below. Note that these are currently specific to UNIX-like environments.

1. Install python (see http://www.python.org).

2. Install NumPy and SciPy (see http://www.scipy.org).

   a. Test that python can access NumPy and SciPy by executing the following commands from the Python prompt:

      import numpy
      import scipy

3. Install and compile the Affymetrix Power Tools. Note that the curl utility and a C compiler must also be installed (most UNIX-like environments have them). A shortcut for installing and compiling is contained in a bash script in the scripts directory. This script can be executed with the following command:

   ./scripts/compile_apt

4. Download and install the library files. This can be down with the following command:

  ./scripts/get_library_files

After these steps have been completed, CEL files can be placed in the "raw" directory and then normalized by executing the "go" script.

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Two-color (long-oligo) arrays and RNA-sequencing data can be processed with the R (http://www.r-project.org) script in code/CalculateProbCodes.R. Transcript lengths and GC content proportions can be specified optionally.

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Please contact Stephen Piccolo (stephen.piccolo@hsc.utah.edu) with questions.