A Short User's Guide of HCE 1.0

Jinwook Seo ( jinwook@cs.umd.edu ) Project Webpage : http://www.cs.umd.edu/hcil/hce/ Human-Computer Interaction Lab ( http://www.cs.umd.edu/hcil/) University of Maryland, College Park

1. Input Data File Format

The extension of your input data to HCE should be .exp. Your data file should be a tab-delimited text file.

2. Load a expression profile data

Click the file open icon on the main tool bar.

Don't forget to check the check box ("Log Scale?") if the data is already in log scale. If you want to do a log-transformation, just uncheck it.

3. Select a linkage method, and check the sample name to cluster

Click OK, and you can see the resulting dendrogram on the screen.

If you want to try a different linkage method,

Click the clustering icon on the main tool bar, and select a different linkage method on the dialog box

4. Switch between Original view and Compressed view

If your data set is so large that the resulting dendrogram cannot be fit in one screen, you can toggle the viewing mode between original and compressed.

	Original view
	Compressed view

5. Using the minimum similarity bar and the detail cutoff bar

 There are two bars in the main view of HCE, one is the minimum similarity bar and the other is the detail cutoff bar. You can drag the minimum similarity bar to change the minimum similarity threshold. You can also drag up the detail cutoff bar to ignore the detail expression level and see the global pattern of the clustering results. You can set the position of the detail cutoff bar to the bottom of the tree by double clicking on the bar - no detail cutoff.

6. Comparison of clustering results

You can compare two clustering results by different linkage methods.

Click the cluster comparison icon on the main tool bar, and select two linkage methods on the dialog box.

You can see the mapping of each gene between the two different clustering results by double-clicking a specific cluster on the first dendrogram.

7. Control Panel Usage

Control Panel	Description
	You can choose 2 samples for X and Y axis respectively, and see the 2D scattergram. It is also possible to quickly browse the scattergrams by dragging the item sliders on each axis. By drawing a rectangle on the scattergram, you can select a group of genes and see where they are located in the dendrogram.
	You can see the histogram for the whole data set. By dragging the green or red vertical lines, you can change the color mapping.
	You can change the bar width of the terminal nodes of the dendrogram from 2 to 10 pixels.

Last updated 11/19/2004

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