Affymetrix miRNA CEL Input Engine

Probe-level intensity data gathered from Affymetrix miRNA microarrays is typically collected and stored in raw data 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 miRNA 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.

•	One or more specific library files, available for download from Affymetrix, that contain information used to associate individual data points extracted from the .cel files with corresponding probesets.

For example, data, select exp_miRNA.sas7bdat as the EDF. This file uses data from three different .cel files, each corresponding to a separate array.

The Sample Data\Microarray\Affymetrix miRNA folder contains both raw data and CDF files.

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 miRNA CEL Input Engine output documentation for detailed descriptions.