Error with GSEA

[Ayushi Mandloi]

Hello,

I am trying to run pre-ranked GSEA on my gene list and I am receiving this error while uploading the file.
<Error Details>

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

---- Stack Trace ----
# of exceptions: 1
------For input string: "?"------
java.lang.NumberFormatException: For input string: "?"
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.RankedListParser.parse(RankedListParser.java:72)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readRankedList(ParserFactory.java:555)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:769)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:735)
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)

[Anthony Castanza]

Hello,

It looks like GSEA encountered an unexpected character value (a ? Symbol) where it expected a number. Could you double check that your file complies with the expected two column, tab delimited, rnk format specification, with gene identifiers in the first column and numeric ranking values in the second column?

If you've double checked and are unable to identify the specific cause of the issue we'd be happy to inspect the file. You could either send it here, or confidentially to the gsea...@broadinstitute.org address.

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

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