Process Description

Affymetrix Tiling BAR Input Engine

The Affymetrix Tiling Bar Input Engine imports and combines raw expression data from Affymetrix BAR files into a single SAS data set that can be used in JMP Genomics analytical procedures (processes).

Note: This input engine does not function in client/server mode.

What do I need?

There are two required files:

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One or more Affymetrix .bar files containing the raw expression data are required as input for this process. These files must be located in the same folder.

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An Experimental Design File (EDF), indexing the .bar files, is required. The EDF lists specific information about the design of the experiment. The EDF is typically a text file or Excel spread sheet or SAS data set and must be created before the data can be imported. The expdesign.sas7bdat EDF is shown below.

The expdesign.sas7bdat file lists 2 pairs of .bar files, each corresponding to a single chip, from the GSE15220 GEO data set downloaded from the NCBI. This file was generated using the Affymetrix Tiling BAR Input Engine.

The following example uses the GSM381561_A-2-samples_analysis_pvalue.bar, GSM381561_A-2-samples_analysis_signal.bar, GSM381562_B-2-samples_analysis_pvalue.bar, and GSM381562_B-2-samples_analysis_signal.bar files. The files were downloaded from the Affymetrix website and placed in a new Bar files directory located in the JMP Genomics Sample Data folder.

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 Tiling BAR Input Engine output documentation for detailed descriptions.