<p>I'm want to perform an GSEA of some RNA-seq data but when I upload the expression data set file this problem appears but I don't know how to solve it.</p>
<p>Thanks for your help.</p>
<p>Pol</p>
<p>Error Details</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>

CC BY-SA 4.0
2024-01-11T14:01:36.730Z
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
CC BY-SA 4.0
2024-01-14T19:32:54.143Z
Please show the first few lines of your input files. Given this is a file format error problem, it will help to know the current format of your files.
gringer
<gsea>
Error in GSEA expresion data set file
# Error in GSEA expresion data set file

(Asked by: username_0 on 2024-01-11)

I'm want to perform an GSEA of some RNA-seq data but when I upload the expression data set file this problem appears but I don't know how to solve it.
Thanks for your help.
Pol
Error Details
---- 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)

**Tags:** gsea
> **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.  
> **username_2**: Please show the first few lines of your input files. Given this is a file format error problem, it will help to know the current format of your files.  

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## 0 answers

