text: user2146: 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)
  
  
  user48: You seem to have forgotten the space after the #. It should be as in here (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
  
  
original_text: 2146: <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>
   48: <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>
  