Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-01-18T22:43:08.970Z
Answers.LastActivityDate: 2022-01-19T10:00:24.590Z
Answers.LastEditDate: 2022-01-19T10:00:24.590Z
Answers.UserDisplayName: Hong
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-22T16:25:38.100Z
Comments.Text: 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.
Comments.UserDisplayName: Mackenzy Radolec
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-01-12T16:58:20.610Z
Comments.Text: Sorry for my delayed response, if you do get chance @Hong please remember to "accept" your answer. Much appreciated.
Comments.UserDisplayName: M__
Tags: <gsea><parsing>
Title: #1 Parsing trouble java.lang.NumberFormatException in GSEA 4.2.1
ThreadText: # #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 @username_0 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.
  
  
  ---
  
  