Answers.Body: <p>You seem to have forgotten the space after the #. It should be as in <a href="http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#CLS:_Categorical_.28e.g_tumor_vs_normal.29_class_file_format_.28.2A.cls.29" rel="nofollow noreferrer">here</a> (Just for future readers know where to find the specs). Also it should be a single line (Maybe this error was introduced while pasting here or it has been a duplicate because there are 39 samples in the 3 line and they should be 37).</p>
  
  <p>Either adding 2 more samples to the initial count and removing the newline of the third line: </p>
  
  <pre><code>39 2 1
  # CD69neg CD69pos
  CD69neg CD69pos CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69pos CD69pos CD69neg CD69neg CD69neg CD69neg CD69pos CD69pos CD69neg CD69pos CD69pos CD69neg CD69neg CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69neg CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69pos CD69pos
  </code></pre>
  
  <p>Or removing the third line:</p>
  
  <pre><code>37 2 1
  # CD69neg CD69pos
  CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69pos CD69pos CD69neg CD69neg CD69neg CD69neg CD69pos CD69pos CD69neg CD69pos CD69pos CD69neg CD69neg CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69neg CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69pos CD69pos
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-07T19:43:48.463Z
Answers.Text: Thank you so much! Yeah the error was about I have multiple columns rather than just one line.
Answers.UserDisplayName: Son nguyen
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-07T20:53:16.923Z
Answers.Text: Glad I could help. Don't forget to mark an answer as accepted or post yourself the solution you find most useful
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-07T15:14:57.050Z
Answers.LastActivityDate: 2018-01-07T15:14:57.050Z
Answers.UserDisplayName: llrs
Body: <p>I am creating a .cls file for my GSEA analysis and see the below error. Can anyone suggest a solution?</p>
  
  <p>I create the file using TeXworks. The file looks like this:</p>
  
  <pre><code>37 2 1
  #CD69neg CD69pos
  CD69neg CD69pos
  CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69pos CD69pos CD69neg CD69neg CD69neg CD69neg CD69pos CD69pos CD69neg CD69pos CD69pos CD69neg CD69neg CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69neg CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69pos CD69pos
  </code></pre>
  
  <h2>Error Details</h2>
  
  <pre><code>---- Full Error Message ----
  There were errors: ERROR(S) #:1 Parsing trouble edu.mit.broad.genome.parsers.Par ...
  
  ---- Stack Trace ----
  
  of exceptions: 1
  ------Number of items found in cls data 10 is not equal to the number specified on the header line 37------ 
  
  edu.mit.broad.genome.parsers.ParserException:
  Number of items found in cls data 10 is not equal to the number specified on the header line 37 at 
  edu.mit.broad.genome.parsers.ClsParser.doSanityChecks(ClsParser.java:388) at 
  edu.mit.broad.genome.parsers.ClsParser._parse_genecluster_style_categorical(ClsParser.java:252) at 
  edu.mit.broad.genome.parsers.ClsParser.parse(ClsParser.java:226) at 
  edu.mit.broad.genome.parsers.ParserFactory._readTemplates(ParserFactory.java:342) at 
  edu.mit.broad.genome.parsers.ParserFactory.readTemplate(ParserFactory.java:293) at 
  edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:753) at 
  edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:726) at 
  edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:52) at 
  javax.swing.SwingWorker$1.call(SwingWorker.java:295) at 
  java.util.concurrent.FutureTask.run(FutureTask.java:266) at 
  javax.swing.SwingWorker.run(SwingWorker.java:334) at 
  java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at 
  java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)
  </code></pre>
  
Tags: <gsea>
Title: GSEA- parsing error for .cls file
ThreadText: # GSEA- parsing error for .cls file
  
  (Asked by: username_0 on 2018-01-06)
  
  I am creating a .cls file for my GSEA analysis and see the below error. Can anyone suggest a solution?
  
  I create the file using TeXworks. The file looks like this:
  
  ```
  37 2 1
  #CD69neg CD69pos
  CD69neg CD69pos
  CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69pos CD69pos CD69neg CD69neg CD69neg CD69neg CD69pos CD69pos CD69neg CD69pos CD69pos CD69neg CD69neg CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69neg CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69pos CD69pos
  
  ```
  
  ## Error Details
  
  ```
  ---- Full Error Message ----
  There were errors: ERROR(S) #:1 Parsing trouble edu.mit.broad.genome.parsers.Par ...
  
  ---- Stack Trace ----
  
  of exceptions: 1
  ------Number of items found in cls data 10 is not equal to the number specified on the header line 37------ 
  
  edu.mit.broad.genome.parsers.ParserException:
  Number of items found in cls data 10 is not equal to the number specified on the header line 37 at 
  edu.mit.broad.genome.parsers.ClsParser.doSanityChecks(ClsParser.java:388) at 
  edu.mit.broad.genome.parsers.ClsParser._parse_genecluster_style_categorical(ClsParser.java:252) at 
  edu.mit.broad.genome.parsers.ClsParser.parse(ClsParser.java:226) at 
  edu.mit.broad.genome.parsers.ParserFactory._readTemplates(ParserFactory.java:342) at 
  edu.mit.broad.genome.parsers.ParserFactory.readTemplate(ParserFactory.java:293) at 
  edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:753) at 
  edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:726) at 
  edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:52) at 
  javax.swing.SwingWorker$1.call(SwingWorker.java:295) at 
  java.util.concurrent.FutureTask.run(FutureTask.java:266) at 
  javax.swing.SwingWorker.run(SwingWorker.java:334) at 
  java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at 
  java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)
  
  ```
  
  **Tags:** gsea
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-01-07. Score: 3
  
  You seem to have forgotten the space after the #. It should be as in [here](http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#CLS:_Categorical_.28e.g_tumor_vs_normal.29_class_file_format_.28.2A.cls.29) (Just for future readers know where to find the specs). Also it should be a single line (Maybe this error was introduced while pasting here or it has been a duplicate because there are 39 samples in the 3 line and they should be 37).
  
  Either adding 2 more samples to the initial count and removing the newline of the third line:
  
  ```
  39 2 1
  # CD69neg CD69pos
  CD69neg CD69pos CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69pos CD69pos CD69neg CD69neg CD69neg CD69neg CD69pos CD69pos CD69neg CD69pos CD69pos CD69neg CD69neg CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69neg CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69pos CD69pos
  
  ```
  
  Or removing the third line:
  
  ```
  37 2 1
  # CD69neg CD69pos
  CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69pos CD69pos CD69neg CD69neg CD69neg CD69neg CD69pos CD69pos CD69neg CD69pos CD69pos CD69neg CD69neg CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69neg CD69neg CD69pos CD69pos CD69pos CD69neg CD69pos CD69pos CD69pos CD69pos
  
  ```
  
  > **Comments:**
  > **username_0**: Thank you so much! Yeah the error was about I have multiple columns rather than just one line.  
  > **username_1**: Glad I could help. Don't forget to mark an answer as accepted or post yourself the solution you find most useful  
  
  ---
  
  