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For more information about the Integrative Genomics Viewer or to connect independently to the IGV home page, see Integrative Genomics Viewer.
. You may also want to refer to the IGV User Guide
. The IGV viewer and the NCI Heat Map viewer both require you to install a version of Java containing Java Web Start. For more information, see #Java for IGV and Heat Map Viewer. |
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- With the appropriate study open, click Heat Map Viewer on the left sidebar. This opens the View Heat Map Viewer Selector page, shown in the following figure.
- Select the appropriate Copy Number Platform in the drop down list.
- The Annotations - Default panel displays existing annotation fields for the gene expression data in the open study. Select one or more annotations in the annotation list. For convenience, you can use the Select All or Unselect All buttons.
- Click View to view the data you select in Heat Map Viewer. caIntegrator creates Heat Map Viewer files of the data.
- After the files are created, click the Launch Heat Map Viewer hypertext link that appears.
Continue with Step 3 in #Method 1 HMV.
Info title HMV help files For interpretation of the results and using HMV features, see the help files opened from HMV.
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To use the IGV and the NCI Heat Map viewer, described in #Viewing Data with the Integrative Genomics Viewer and #Viewing Data with Heat Map Viewer, you must install a version of Java containing Java Web Start. You must install recent versions of the Java Development Kit (JDK 1.5.0 aka JDK 5.0 or newer) or Java Runtime Environment (JRE 1.5.0 aka JRE 5.0 or newer). The easiest option is to install JRE 5.0
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Without Java Web Start, when you click Launch Integrative Genomics Viewer or Launch Heat Map Viewer, a dialog box displays in your browser giving you the option to save or open with igv.jnlp (IGV) or retrieveFile.jnlp (HMV). Clicking the Open option starts the Java Web Start Launcher (default), installing the Java app so that you can view the files.
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