Affymetrix Exon CHP Input Engine

Probe-level intensity data gathered from Affymetrix microarrays is typically collected and stored in raw data files formatted as .chp files. Before the information contained in these files can be manipulated and analyzed using JMP Genomics, it must be extracted and organized into two SAS data sets:

•	one tall data set containing all of the raw data, and

•	an Experimental Design Data Set (EDDS) , that contains information about the experimental design.

The Affymetrix Exon CHP Input Engine imports and combines raw Affymetrix .chp exon expression files into a single SAS data set and generates an EDDS.

What do I need?

Before you can successfully import the raw data into SAS data sets that can be used for analysis in JMP Genomics, you must locate and gather three different sources of information:

•	The folder containing the raw data files. These .chp files, each corresponding to an individual microarray, contain the hybridization intensities.

•	The Experimental Design File (EDF) for the experiment. The EDF lists specific information about the design of the experiment. The EDF is typically a text file or Excel spread sheet and must be created before the data can be imported.

•	A specific meta probeset library file, available for download from Affymetrix, that contains information used to associate individual data points extracted from the .chp files with corresponding probesets.

The following example uses a subset, corresponding to two arrays, of the Affymetrix Human Exon 1.0 ST colon cancer data set downloaded from http://www.affymetrix.com/support/technical/sample_data/exon_array_data.affx and shipped with JMP Genomics.

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

Output/Results

The output data sets generated by this process are listed in a Results window. Refer to the Affymetrix Exon CHP Input Engine output documentation for detailed descriptions.