I am using cytoscape 3.8.1. I used the output from GSEA to vizualise the network in EnrichmentMap app. After that I tried Analyze network to know the node degree, closeness centrality etc. to identify hub genes. But when I run Analyse network it gives error as "network interpretation null". If I try the same with sample yeast network it works. Can anyone suggest what could be the reason for the error? Thank you.
Greetings, I assume you are running Cytoscape 3.8.0 since Cytoscape 3.8.1 hasn't been released (or even branched) yet. Are you trying to analyze the original network or the enrichment map? That will help us diagnose the problem. Also, if you could run Cytoscape from the command line and let us know if any stack trace happens, that would help also.