<p>I just figured out the error. My .TXT was not correctly formated, following the instruction from <a href="https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#Expression_Data_Formats" rel="nofollow noreferrer">their manual</a> under .TXT format worked.</p>

CC BY-SA 4.0
2022-01-18T22:43:08.970Z
2022-01-19T10:00:24.590Z
2022-01-19T10:00:24.590Z
Hong
<p>I am getting the following error message when I tried to load .TXT data file to GSEA 4.2.1.  I tried different way to change the file name as .GCT but not working.  Any suggestion? Many thanks.</p>
<p>Full Error Message:</p>
<pre><code>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:266)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.parseFieldsIntoFloatArray(AbstractParser.java:371)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.parseTextMatrixToDataset(AbstractParser.java:293)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:109)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readDatasetTXT(ParserFactory.java:201)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:760)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:737)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:52)
    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
2023-05-22T16:25:38.100Z
Can you elaborate on what was not correctly formatted? I followed the instruction on their manual .txt and am getting this same error. Thank you.
Mackenzy Radolec
CC BY-SA 4.0
2024-01-12T16:58:20.610Z
Sorry for my delayed response, if you do get chance @Hong please remember to "accept" your answer. Much appreciated.
M__
<gsea><parsing>
#1 Parsing trouble java.lang.NumberFormatException in GSEA 4.2.1
# #1 Parsing trouble java.lang.NumberFormatException in GSEA 4.2.1

(Asked by: username_0 on 2022-01-18)

I am getting the following error message when I tried to load .TXT data file to GSEA 4.2.1.  I tried different way to change the file name as .GCT but not working.  Any suggestion? Many thanks.
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:266)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.parseFieldsIntoFloatArray(AbstractParser.java:371)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.parseTextMatrixToDataset(AbstractParser.java:293)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:109)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readDatasetTXT(ParserFactory.java:201)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:760)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:737)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:52)
    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, parsing
> **Comments:**
> **username_1**: Can you elaborate on what was not correctly formatted? I followed the instruction on their manual .txt and am getting this same error. Thank you.  
> **username_2**: Sorry for my delayed response, if you do get chance @Hong please remember to "accept" your answer. Much appreciated.  

---

## 1 answers

### Answer by username_0 on 2022-01-18. Score: 2

I just figured out the error. My .TXT was not correctly formated, following the instruction from [their manual](https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#Expression_Data_Formats) under .TXT format worked.


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