Comments (3)
What is the format of the header row of your files? It looks like EM is assuming that GSEA results have 11 columns.
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here is the header row for fGSEA results that I have created -
name description GS details SIZE ES NES pval padj FWER Rank at Max leading edge genes
(truthfully I am not sure which file the above is referring to but I have a generic method for creating fGSEA results and they all look like this)
from enrichmentmapapp.
Hi Ruth,
What is the actual problem? I just tried creating a network from a GSEA data set and I swapped the positive and negative files and it appears to still have worked.
from enrichmentmapapp.
Related Issues (20)
- CreateEMNetworkTask should be cancellable
- ability to layout network by dataset
- The enrichmentmap build command always creates 2 datasets when a gmt file is provided
- Different results when running via CLI vs. CyREST HOT 3
- If rank file starts with empty line get error
- GSEA-Enrichmentmap-Cytoscape-desktop applicaion HOT 4
- Diffuse string Network HOT 1
- User unaware that multi-dataset maps are supported HOT 1
- EM version 3.4.0-SNAPSHOT" Default style node color: -log10(pvalue)_max (enhancement) HOT 8
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- Input files for EnrichmentMap HOT 3
- create a subnetwork of most significant gene set per cluster HOT 6
- Issue with Parsing .txt or .xls Files in EnrichmentMap: "For input string: 'I<' Error" HOT 3
- No documentation discussing how to create EM from just gmt file HOT 2
- issue installing new version of EM app if you installed through EM collection HOT 1
- running enrichmentmap build command doesn't create new default visualization HOT 1
- mastermap with commands from docker does not work
- checkbox in creation dialog for running AA
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