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Choosing Nested EASE Parameters
After loading the analysis file, click the Meta-Analysis drop-down menu, and select EASE Cluster Analysis. An initialization dialog will appear.
Step 1: Selecting the EASE file system
To manually load an EASE file system click the button marked Custom in the EASE Annotation Analysis dialog which will bring up the EASE Advanced Parameters dialog, then click the Browse button. Proceed to navigate to the folder you previously downloaded, nease_example_files. Inside it, open the folder named data\ease\affy_HT_HG-U133A_EASE. You should see three folders inside, Data, Enhance and Lists. Do not select any of these folders. Simply click Open.
Make sure the option Select Background Population from File is selected in the EASE Advanced Parameter dialog. Click the button labeled File Browser in the Population panel and select the file Lists/affy_HT_HG-U133A/Populations/ProbesetIDs.txt.
Step 3: Annotation Parameter Selection
From the drop-down menu labeled Annotation Key in the MeV Annotation Key panel, select the heading PROBE_ID. Click the checkbox labeled Use Annotation Converter. Click the button labeled File Browser. The file selection dialog that opens should already be set to the correct directory. (If it is not, navigate to nease_example_files\affy_HT_HG-U133A_EASE\Data\Convert.) Select the file affy_HT_HG-U133A_ProbesetIDs.txt and click Open. Under the heading Gene Annotation /Gene Ontology Linking Files, click the Add Files button. Again, the resulting file browser should already be displaying a list of the available GO term files. (If not, navigate to nease_example_files\affy_HT_HG-U133A_EASE \Data\Class directory within the MeV folder.) Hold down the control key and click on the files GO Biological Process.txt, GO Molecular Function.txt and GO Cellular Component.txt to select them. When the three files are selected, click Open.
Click the OK button to return the the main EASE dialog.
Click to select the check box next to Run Nested EASE, near the bottom of the EASE Annotation Analysis dialog. Now click the Ok button to run EASE and Nested EASE. This will take some time.