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- With the appropriate study open, click Integrative Genomics Viewer on the left sidebar. This opens the View IGV Selector page, shown in the following figure.
- In the drop-down list, select the Gene Expression Platform for the data you want to view.
- Select the Copy Number Platform ID.
- The Annotations - Default panel displays existing annotation fields for the gene expression data in the open study. Select those fields you want to view when you open the IGV. Use the buttons for convenience if you want to Select All or Unselect All, when all are checked.
- Click View to see the data in the Integrative Genomic Viewer. caIntegrator creates IGV files of the data.
- After the files are created, click the Launch Integrative Viewer hypertext link that appears.
- Continue with Step 3 in #Method Method 1 IGV.
Viewing Data with Heat Map Viewer
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For more information about the Heat Map Viewer or to connect independently to the HMV home page, see Heat Map Viewer documentation or HMV documentation. 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 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 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 Viewing Data with the Integrative Genomics Viewer and #Viewing 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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