new error message

[Marcia Maldonado]

<Error Details>

---- Full Error Message ----
col:5 > matrix's fColCnt:5

---- Stack Trace ----
# of exceptions: 1
------col:5 > matrix's fColCnt:5------
java.lang.ArrayIndexOutOfBoundsException: col:5 > matrix's fColCnt:5
at org.gsea_msigdb.gsea/edu.mit.broad.genome.math.Matrix.getColumnV(Matrix.java:261)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.DefaultDataset.getColumn(DefaultDataset.java:289)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateFactory.extract(TemplateFactory.java:85)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.alg.DatasetGenerators.extract(DatasetGenerators.java:292)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.alg.DatasetGenerators.extract(DatasetGenerators.java:288)
at org.gsea_msigdb.gsea/xtools.gsea.AbstractGsea2Tool.execute_one(AbstractGsea2Tool.java:79)
at org.gsea_msigdb.gsea/xtools.gsea.AbstractGsea2Tool.execute_one_with_reporting(AbstractGsea2Tool.java:103)
at org.gsea_msigdb.gsea/xtools.gsea.Gsea.execute(Gsea.java:166)
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]

Hi Marcia,

This would appear to be a structural issue with one of your dataset files.

Could you review the documentation here and ensure your files are compliant? https://docs.gsea-msigdb.org/#GSEA/Data_Formats/

The GSEA software is rather strict about file extensions as well which can cause issues.

Based on the information you sent in your previous message one of your files appears to have a .txt extension, you'd need to make sure it's in specifically the .txt format we describe.

Finally, that doesn't appear to be the correct chip file, the one you selected is for a specific type of Illumina microarrays, for RNA-seq you generally want the Ensembl Gene ID, or Gene Symbol Remapping, chip files.

If you're still having errors after double checking against the documentation please let me know. We'd also be happy to review any of your input files. You can either provide them directly, or confidentially to the gsea...@broadinsitute.org address (we'd only use them for debugging).

Hope this helps

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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