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Viewing the nEASE results
The standard EASE analysis, as described in Hosack, et al. (2003), will run, followed by the Nested EASE analysis. The nEASE results are included as part of the standard EASE results, as a subnode on the result tree, labeled Nested EASE. Double-click the result node labeled EASE Analysis to see the nested ease results appear. We recommend that you expand the size of the window containing the Result Tree by clicking and dragging on the dividing bar between the Result Tree and the larger viewing window on the right. Click on the result nodes to explore the result data within.
The most useful view is found in a node labeled Nested EASE Summary Table, which contains the summarized data for all of the nEASE results. These are the data reported in the manuscript. To examine the genes which drive a result row in the nEASE Summary Table, left-click to select a row, and right-click to open up a context-sensitive menu. Choose Open Viewer -> Expression Image. MeV will open a heatmap view of the probe expression values that correspond to the genes that were members of that group.
All of the usual heatmap-related options are available in this window, including adjusting the color display, changing the gene annotation displayed, and storing the displayed genes in a new cluster. Note that the left-hand panel, the Result Tree, does not obviously change when this heatmap is opened. However, scrolling the Result Tree down will reveal that a new result node has been selected, corresponding to the Nested EASE result that was selected from the Summary Table.
References D. A. Hosack, G. Dennis, B. T. Sherman, H. C. Lane, R. A. Lempicki, Genome Biol 4 (2003). A. J. Minn, et al. , Nature 436, 518. (2005) L. D. Miller, et al. , Proceedings of the National Academy of Sciences 102, 13550 (2005).