Error in file not found

[TMU李沅庭]

I already upload the .GCT and .cls files successfully

However, when I ran GSEA and chose the phenotype, It showed file not found.

How can I deal with it? Thanks

<Error Details>

---- Full Error Message ----
File not found:

---- Stack Trace ----
# of exceptions: 1
------File not found: 
java.io.FileNotFoundException: 
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.createInputStream(ParserFactory.java:1058)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readTemplate(ParserFactory.java:271)
at org.gsea_msigdb.gsea/xtools.api.param.TemplateSingleChooserParam._getTemplates(TemplateSingleChooserParam.java:132)
at org.gsea_msigdb.gsea/xtools.api.param.TemplateSingleChooserParam.getTemplate(TemplateSingleChooserParam.java:46)
at org.gsea_msigdb.gsea/xtools.gsea.Gsea.execute(Gsea.java:126)
at org.gsea_msigdb.gsea/edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:391)
at java.base/java.lang.Thread.run(Unknown Source)

[Anthony Castanza]

Hello,

Would you be able to share the CLS file you produced? It seem that something about its formatting is causing the parser to choke even though (as you stated) it loaded without error.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Anthony Castanza]

Hello,

I received the files you sent via Google Drive. I was able to load them into GSEA without issue and the files correctly populated in the dropdown menu. I'd suggest that perhaps you check the file path to the directory to ensure that it doesn't have any special characters.

That said, with only two samples in the data, I'd recommend computing the differential ranking metric outside GSEA and instead providing the resulting data as a .rnk file to GSEA's Preranked method. The standard method is really intended to handle data with many replicates and running through Preranked with an externally computed metric will simplify the GSEA configuration significantly.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego