Process Description

Export to Affymetrix CHP Format

The Export to Affymetrix CHP Format process exports a SAS data set as a series of Affymetrix .chp files. These files, which contain summarized or otherwise analyzed data, can be shared among colleagues who might not have access to JMP Genomics, but who can open, view, and manipulate the data using Affymetrix or other 3rd-party software.

What do I need?

Two data sets are required for this process:

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A SAS Input Data Set containing all of the experimental data. The affymetrixlatin_norm_mmei.sas7bdat sample data set, contained in the \LifeSciences\Sample Data\Microarray\Affymetrix Latin Square folder that is included with JMP Genomics, serves as an example and is shown below. This data set contains summarized data from the Affymetrix Latin Square data set (described in Affymetrix Latin Square Data), normalized, and subjected to mixed model analysis. Note that this is a tall data set: genes or probesets are listed in rows, and chips are listed in columns.

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The Experimental Design Data Set (EDDS). The affylatin_exp.sas7bdat EDDS serves as an example, and is shown below. This data set tells how the experiment was performed, providing information about the columns in the input data set. The EDDS provides names for the output .chp files. Note that one column in the EDDS must be named ColumnName, and the values contained in this column must exactly match the column names in the input data set.

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

Output/Results

The results of the Export to Affymetrix CHP Format process are displayed in a Message window, shown below.

This process generated 59 separate .chp files. These files can now be sent to and shared with your colleagues.