jActiveModules Z-scores and activepathScores

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segerde...@gmail.com

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May 15, 2018, 5:43:45 PM5/15/18
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Hello -- I am using jActiveModules with Cytoscape 3.6 to identify active subnetworks in an interaction network generated by the CHAT plugin. I would like to see the z-scores for each module. The jActiveModules help document at https://github.com/idekerlab/jActiveModules/wiki/Help says the following:

"Shortly, the Results panel will appear, as illustrated in Figure 5. This window contains a table in which each row represents one putative module, listed according to the number of nodes, and an associated z-score. Z-scores greater than 3.0 are generally considered significant."

- I don't see this in any tab on my Results panel even after selecting any of the jActiveModules-generated networks in the control panel. The Results panel still only displays the original CHAT network. How do I find the z-scores?

- The node table contains a column with the activepathScore for each node/module. How should this be interpreted?

- In general, the help documentation cited above seems a bit out of date (for example, there is no figure on that page). Is there a newer reference or manual available for jActiveModules someplace?

Thanks,
Erik
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