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Chih Long Liu

Walkthrough TMA-Deconvoluter - 4

Open the TreeView program. If you don't have it, download it from http://rana.lbl.gov/EisenSoftware.htm.

Go to File -> Open, and open your newly clustered file (e.g. 4.cdt, in this example). You may adjust the thumbnail and zoom image pixel size (defined for each individual datapoint, represented by a single block of color) to your preferences. You will also need to adjust the contrast to 2 (representing a dynamic range of 2-fold induction or 2-fold repression in gene microarrays, for which TreeView was originally designed).

Treeview Options

TreeView Options

If you use the parameters indicated in the screenshot above, and using the demo file 4.cdt, you should get the following:

TreeView Program Screenshot

TreeView Proram Screenshot

on the image for a larger view of the picture.

You may recall that the scoring data is represented in the following manner:

Score Description Treeview
  Missing datapoint    
0 Negative -2  
1 equivocal/uninterpretable 0  
2 weak 1  
3 strong 2  

You may now browse your dataset for additional analysis. To use TreeView with Stainfinder, proceed to the walkthrough link below.

Back to Step 3.

Walkthrough for setting up Stainfinder

Return to the walkthrough overview page.

Last edited by Chih Long Liu on January 17, 2007