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I've made my files for a GSEA ANALYSIS, but the software gives me this error:

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

---- Stack Trace ----
# of exceptions: 1
------For input string: "description"------
java.lang.NumberFormatException: For input string: "description"
    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)

These are the first lines of my file, made up by 18839 rows of genes:

#1.2                                        
18839   9                                   
NAME    description ASPC1   CFPAC1  HS766T  BXPC3   CAPAN1  HPAFII  PANC0813    PaTu8902    SU8686
A1BG    NA  0.13750352  0.15055968  0.16349873  0   0.37851162  0.01435529  0   0.01435529  2.10433666
A1CF    NA  3.45285896  0.08406426  0.05658353  0   0.32192809  2.1210154   0.01435529  0   0.04264434
A2M NA  0.07038933  0.20163386  0.48542683  0.21412481  0.05658353  0.04264434  0.20163386  0.05658353  0.15055968
A2ML1   NA  0.01435529  0.01435529  0   1.88752527  0.21412481  0.02856915  2.70708299  2.63459327  0.71369581
A3GALT2 NA  0.02856915  0   0   0   0   0.02856915  0.04264434  0.02856915  0
A4GALT  NA  3.46466827  3.36176836  3.09423607  4.22573765  2.50589093  3.61941301  3.21723072  0.01435529  3.34198575
A4GNT   NA  0   0   0   0   0   0   0   0.01435529  0.26303441
```
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  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Commented May 9 at 11:58

1 Answer 1

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A similar error has been described in the past and attributed to the presence of missing observations in the data.

Have you checked your data and tried to look for e.g. NA values? It seems that GSEA does not work with missing data.

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