Process Description

Affymetrix ARR File Parser

Investigators receiving data from core lab facilities that use the Affymetrix Gene Chip Command Console 3 (AGCC) often find that information about the experiments is stored in a series of XML-based .arr files. Normally, a separate .arr file is associated with each .chp file. The Affymetrix ARR File Parser process is a JMP Scripting Language (JSL) script that parses information from all of the .arr files into two JMP files:

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The first output file (named ARR.jmp, by default) contains all the experimental parameters listed in all of the .arr files.

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The second output file (named EDF.jmp, by default) lists only those variables that vary across chips. This EDF.jmp file can be modified to serve as an Experimental Design File (EDF) for subsequent JMP Genomics processes.

Creating an Experimental Design File (EDF) is often the most troublesome task in preparing your data for analysis with JMP Genomics. The Affymetrix ARR File Parser process can help expedite creation of your experimental design file.

What do I need?

To run this process, you need all of the .arr files, from the experiment, in the same folder.

The MPRO GCC Hourly demo data set provided by Affymetrix can serve as an example. The compressed files were downloaded from the Affymetrix website (www.affymetrix.com), unzipped and saved to a folder.

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

Output/Results

Refer to the Affymetrix ARR File Parser output documentation for a detailed description of the output of this process.