Re: Error running GSEA

[Prakash Kulkarni]

Hello,

I am working on Proteomics data. I have followed the Nature Protocol Article 

• https://doi.org/10.1038/s41596-018-0103-9. Where I used g: profiler to generate the GMT file. After generating the file and loading it into GSEA, the following error message occurred. Could you help me solve the issue?

<Error Details>

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

---- Stack Trace ----
# of exceptions: 1
------For input string: "P05198,O43670,Q92973,P25705,P62241,P0DMV9,Q14103,P04075,Q00839,P19338,P31943,Q07666,P27797,Q13148,P60900,P62244,P62269,P62851,Q9H1E3,Q9NR30"------
java.lang.NumberFormatException: For input string: "P05198,O43670,Q92973,P25705,P62241,P0DMV9,Q14103,P04075,Q00839,P19338,P31943,Q07666,P27797,Q13148,P60900,P62244,P62269,P62851,Q9H1E3,Q9NR30"
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:200)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:758)
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)

[Castanza, Anthony]

Hello,

It looks like the GMT file produced by g:profiler is improperly formatted using comma delimited strings instead of tab delimited strings. We do not produce g:profiler, so I would recommend checking their documentation to see if this can be corrected.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

--
You received this message because you are subscribed to the Google Groups "gsea-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gsea-help+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/588d27c2-2b32-43fe-a0c7-de1f0452b919n%40googlegroups.com.