![]() Maybe go thumbs-up this comment in the EnrichmentMap issue tracker, if you think the maintainers need to work on that. Hopefully this benefits someone who ends up here after googling for "Unable to create Enrichment Map:Internal Server ErrorResponseEntityProxy," which is just a stupendously unhelpful error message when "None of the gene sets have passed the filter" is actually what went wrong. My problem was that GSEA's default cutoffs (p-value < 0.005 and FDR Q-value < 0.1) were entirely too stringent for my results set, and using the "Very permissive" settings of p-value < 0.05 and FDR < 0.25 from the documentation solved it for me. In the GSEA application logs, then you would've had the problem described in EnrichmentMap's GitHub issue #358, and the solution would be to use less stringent p- and FDR Q-value cutoffs, as prescribed in the " Tips on Parameter Choice" section of the EnrichmentMap documentation. Try relaxing the gene set filter parameters. If you had seen the error message None of the gene sets have passed the filter. I know that's lame, but sometimes that's how you solve weird computer errors, when the error message the application itself gives you is non-specific and unhelpful. lastly, try reinstalling everything on a completely different machine/OS and see if you get different results ( e.g., try on a Mac or Linux if you had problems with Windows originally, or vice-versa).update to the latest Java 8, reinstall Cytoscape 3.7.whatever and the EnrichmentMap plugin from scratch, and re-download GSEA, -or.try closing all the programs, restarting them, possibly rebooting and restarting them, and even analyzing a completely different set of data to see if you get the same results, -or.My recommendations to you at the time would've been This is a tough one, because the only relevant lines from your GSEA debug log were these two: DEBUG - http-outgoing-4 << "Failed: empty String"ĭEBUG - http-outgoing-4 << HTTP/1.1 500 Internal Server Error INFO - Get URL: DEBUG - CookieSpec selected: defaultĭEBUG - Auth cache not set in the contextĭEBUG - Connection request: [route: ĭEBUG - Connection manager is shutting downĭEBUG - http-outgoing-4: Close connection INFO - successfully connected to cytoscape rest This would show you negative correlations but not all the underlying correlations between the features with make up a module.I am trying to visualize a GSEA analysis I conducted using the Broad Institute's GSEA Enrichment Map Visualization, however I get the following error and am not sure what the issue is: any help would be greatly appreciated. qza to get a correlation network where modules are represented as a single node. Then run build-correlation-network-r or build-correlation-network-p with that correlation. qza from make-modules-on-correlations to run calculate-correlations. If you want to see negative correlations and modules then you can use cytoscape to export the module data from the network.gml from make-modules-on-correlations and then add it to the network.gml from build-correlation-network-r or build-correlation-network-p.Īlternatively you could use the summarized feature table. This will not show you your modules though. qza which you create from build-correlation-network-r or build-correlation-network-p. One of the most fundamental tools for interpreting molecular interaction data is visualization of nodes and edges as a two- dimensional network (Tollis et al. If you want to see your network without modules then you can export the network.gml from the. Module making does not include negative edges because you do not want negatively correlated features in the same modules as it would mess up summarization of the features in them. Are you visualizing the network.gml file that comes from running make-modules-on-correlations or from build-correlation-network-r? The network that results from make-modules-on-correlations does not include negative edges because it is showing the network that was used to generate modules.
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