<p>A similar error <a href="https://groups.google.com/g/gsea-help/c/VZzpOlbl5Ow?pli=1" rel="nofollow noreferrer">has been described in the past</a> and attributed to the presence of missing observations in the data.</p>
<p>Have you checked your data and tried to look for e.g. <code>NA</code> values? It seems that GSEA does not work with missing data.</p>

CC BY-SA 4.0
2024-05-10T17:20:17.383Z
2024-05-10T17:20:17.383Z
Maximilian Press
<p>I've made my files for a GSEA ANALYSIS, but the software gives me this error:</p>
<pre><code>---- Full Error Message ----
There were errors: ERROR(S) #:1
Parsing trouble
java.lang.NumberFormatException: ...

---- Stack Trace ----
# of exceptions: 1
------For input string: &quot;description&quot;------
java.lang.NumberFormatException: For input string: &quot;description&quot;
    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<span class="math-container">$1.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.desktop/javax.swing.SwingWorker.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$</span>Worker.run(Unknown Source)
    at java.base/java.lang.Thread.run(Unknown Source)

</code></pre>
<p>These are the first lines of my file, made up by 18839 rows of genes:</p>
<pre><code>#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
<span class="math-container">```</span>
</code></pre>

CC BY-SA 4.0
2024-05-09T11:58:17.923Z
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.
Community
<gsea><errors><data>
Error in Load Data in GSEA 4.3.3
# Error in Load Data in GSEA 4.3.3

(Asked by: username_0 on 2024-05-09)

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
```

**Tags:** gsea, errors, data
> **Comments:**
> **username_1**: 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.  

---

## 1 answers

### Answer by username_2 on 2024-05-10. Score: 0

A similar error [has been described in the past](https://groups.google.com/g/gsea-help/c/VZzpOlbl5Ow?pli=1) 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.


---

