kappa score matrix
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Ilse van Grevenhof
Jun 10, 2016, 5:29:18 AM6/10/16
to cytoscape-helpdesk
I would like to produce a kappa score matrix (visualized) but I am a beginner in terms of ClueGO. How can I produce one?
Bernhard
Jun 10, 2016, 10:11:55 AM6/10/16
to cytoscape-helpdesk
Hi Ilse,
after you have created a ClueGO network you can save all the relevant output files into a project folder. To do this see down the steps on the attached screen shot. In the saved folder you can find then the .txt file with the kappascore values for your network. This is a simple tab delimited text file that you can open with Excel/Openoffice. To visualize the heatmap like in the ClueGO tutorial you can use a variety of software tools for clustering data. One of them is Genesis which you can download here: http://genome.tugraz.at/genesisclient/genesisclient_download.shtml
Just open the kappascore matrix txt with Genesis and then click on HCL for hierarchical clustering in the toolbar then you should get a nice kappa score heatmap.
Best
after you have created a ClueGO network you can save all the relevant output files into a project folder. To do this see down the steps on the attached screen shot. In the saved folder you can find then the .txt file with the kappascore values for your network. This is a simple tab delimited text file that you can open with Excel/Openoffice. To visualize the heatmap like in the ClueGO tutorial you can use a variety of software tools for clustering data. One of them is Genesis which you can download here: http://genome.tugraz.at/genesisclient/genesisclient_download.shtml
Just open the kappascore matrix txt with Genesis and then click on HCL for hierarchical clustering in the toolbar then you should get a nice kappa score heatmap.
Best
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