Process Description
Affymetrix Expression CEL Input Engine
Probe-level intensity data gathered from Affymetrix microarrays is typically collected and stored in raw data files formatted as .cel 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 Expression CEL Input Engine enables you to import data and other information contained in Affymetrix .cel files into these SAS data sets.
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 .cel 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. |
The following example uses Affymetrix Latin Square Data. Data is spread across 59 different .cel files, each corresponding to a separate array.
The DesignTable.txt file has been selected as the EDF.
The HG_U95A_trim.CDF file, which is included with JMP Genomics, is located in the Affymetrix Latin Square folder and serves as the library file for this example.
For detailed information about the files and data sets used or created by JMP Genomics 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 Expression CEL Input Engine output documentation for detailed descriptions.