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GSEA-MSigDB/gsea-desktop
Pop Specialized Error Message when loading file with UTF-16 Text Encoding

GSEA expects UTF-8 text, however UTF-16 encoded gene set files can load without obvious errors. This then manifests during the analysis as being unable to match genes. An error message when attempting ...
  • ACastanza
  • Opened 
    on Nov 13, 2024
  • #71

GSEA-MSigDB/gsea-desktop
Report Missing Random Seed with No Collapse

When Running GSEA, if no collapse is selected, then it appears that the GSEA report index does not include the Comments section, which results in the report failing to include the value used for the Random ...
  • ACastanza
  • Opened 
    on Sep 26, 2024
  • #70

GSEA-MSigDB/gsea-desktop
Move Enrichment statistic Parameter to Advanced Fields

Generally users should not be modifying this parameter, however it is currently in Basic Fields which gives users the mistaken assumption that adjustments to this parameter are something that should be ...
  • ACastanza
  • Opened 
    on Sep 13, 2024
  • #69

GSEA-MSigDB/gsea-desktop
Export Dataset GCT After Collapse

Numerous downstream applications would benefit from the access to the post-collapse gene expression data. Ideally this would be written to the same folder as the ranked list.
  • ACastanza
  • Opened 
    on Aug 27, 2024
  • #68

GSEA-MSigDB/gsea-desktop
Duplicate Values in Continuous Expression Profiles Error

Issue uncovered by Konstantin on the forums: unnamed This behavior makes sense from the perspective of time-series data (which is what this mode was, in fact, originally designed for), however for other ...
  • ACastanza
  • Opened 
    on Mar 6, 2024
  • #67

GSEA-MSigDB/gsea-desktop
Unable to load desktop app on Mac

Hello, I installed the GSEA desktop app but have encounter an error on a Mac device running Sonoma 14.0. The error says GSEA quit unexpectedly . I tried on a different Mac running Ventura 13.5.2 and it ...
  • mtageldein
  • 4
  • Opened 
    on Feb 13, 2024
  • #66

GSEA-MSigDB/gsea-desktop
Ranked list are zero-indexed; should be one-indexed

Michael Reich noticed the Ranked list display in GSEAPreranked are being shown with a zero-index start, which is a little non-intuitive for most users.
  • davideby
  • Opened 
    on Aug 6, 2023
  • #65

GSEA-MSigDB/gsea-desktop
Document command line options

These were never spelled out in the documentation but instead left as something for discovery through the Command feature. We should capture these in the User Guide. It might also be useful to capture ...
  • davideby
  • Opened 
    on Jul 21, 2023
  • #64

GSEA-MSigDB/gsea-desktop
Poor error message on nearly-complete pruning on Collapse

This was reported by Michael Reich. There s an odd corner case with an unintended error message for a Collapse that results in a nearly-complete (but not *totally-complete) pruning: openjdk version 11.0.3 ...
  • davideby
  • Opened 
    on Jul 8, 2023
  • #63

GSEA-MSigDB/gsea-desktop
Improve warning message for mix of local/remote GMT & CHIP

It s possible that we should take another look at the warning/error messages around this. This was pointed out on the forum by someone who had downloaded a Gene Set GMT off the website. Perhaps we don ...
  • davideby
  • Opened 
    on May 2, 2023
  • #62
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