"Parsing trouble" error during annotation file download

[Thomas Hunaut]

Hello, 

I'm using GSEA v4.4.0 on Windows. I tried to load my annotation file in GSEA but there is an error message: 

<Error Details>

---- Full Error Message ----
There were errors: ERROR(S) #:1
Parsing trouble
java.lang.NumberFormatException: For input string: "ATAD3B"
 ...

---- Stack Trace ----
# of exceptions: 1
------For input string: "ATAD3B"------
java.lang.NumberFormatException: For input string: "ATAD3B"
at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(Unknown Source)
at java.base/jdk.internal.math.FloatingDecimal.parseFloat(Unknown Source)
at java.base/java.lang.Float.parseFloat(Unknown Source)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.parseStringToFloat(AbstractParser.java:250)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.parseFieldsIntoFloatArray(AbstractParser.java:361)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.parseTextMatrixToDataset(AbstractParser.java:277)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:108)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readDatasetTXT(ParserFactory.java:201)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:759)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:736)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:53)
at java.desktop/javax.swing.SwingWorker$1.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.desktop/javax.swing.SwingWorker.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)

I've read the advice you gave to others having the same problem but I couldn't find a way to solve my problem. 

Can you help me

Thanks 

Thomas

[Anthony Castanza]

Hi Thomas,

Our apologies for the spam email that slipped through our filters over the weekend.

To answer your question, this error occurs because the formatting of your file doesn't match the expected structure of the file type you've provided to the GSEA software.

Based on the message text, the file you used was a ".txt" file. GSEA's specific formatting requirements for .txt files are fairly rigid. They're detailed here in our user guide: https://docs.gsea-msigdb.org/#GSEA/Data_Formats/#txt-text-file-format-for-expression-dataset-txt

If, after checking your file against the documentation there, you're still encountering errors, please let us know and we'd be happy to take a look.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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