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New Affymetrix Expression CHP Wizard Streamlines Analysis Workflow

JMP Genomics 3.1 includes a new streamlined application for the analysis of Affymetrix CHP files, the Affymetrix Expression CHP Wizard. The wizard is designed to quickly introduce new users to a typical expression analysis workflow in JMP Genomics. This new tool uses an interactive interface to collect required information about an Affymetrix microarray experiment, and automatically constructs a JMP Genomics workflow behind the scenes to perform import, QC and analysis of the data set using the JMP Genomics Workflow Builder.

Workflow Builder, first introduced in JMP Genomics 3.0, allows users to string together multiple process settings to run in sequence. Output is presented in a JMP journal, containing buttons that launch results scripts from all processes included in a workflow. Users may save, modify and reuse workflows created through the Workflow Builder, or the Affymetrix Expression CHP Wizard. For those of you who want the details, the interactive interface of the Affymetrix Expression CHP Wizard interface was created as a JSL script which calls SAS, interacts with NetAffx, and runs the Workflow Builder application as needed to create results.

The typical microarray analysis workflow run by the Affymetrix Expression CHP Wizard contains the following steps:

• Import of CHP files and design information.

• Automatic download of annotation files (if desired) and library files (if required, as for older CHP formats) from the Affymetrix NetAffx Web site.

• Quality control processes to view intensity distributions, correlation among replicates, and 2-D and 3-D PCA plots.

• ANOVA for relatively simple experimental designs with one or two factors and one blocking variable.

• Upload of results to Ingenuity Pathway Analysis (IPA) for further exploration.

The Affymetrix Expression CHP Wizard was designed with input from Affymetrix, specifically with users of the new Affymetrix Command Console and Expression Console in mind. The most streamlined wizard workflow automatically extracts design information from Affymetrix array attribute (ARR) files, paired with CHP files containing normalized data output from Expression Console. For older CHP file versions, wizard users may provide experimental design information in the form of an existing JMP Genomics experimental design file or text file containing file names.

Even users already familiar with JMP Genomics will appreciate the streamlined wizard interface. It also makes an ideal tool for teaching students the basics of microarray analysis, or for researchers who wish to analyze CHP files generated by a core lab.

A special thanks to Tzu-Ming Chu, who spent many hours working on making the Affymetrix Expression CHP Wizard a reality, and to Stan Martin, who worked on implementing the NetAffx download capabilities in JMP Genomics 3.1.

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