<p>I get the following error when I try to load a .chip file to <a href="https://www.gsea-msigdb.org/gsea/index.jsp" rel="nofollow noreferrer">GSEA</a> software. What is the problem?</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;YBL028C&quot;------
java.lang.NumberFormatException: For input string: &quot;YBL028C&quot;
    at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source)
    at sun.misc.FloatingDecimal.parseFloat(Unknown Source)
    at java.lang.Float.parseFloat(Unknown Source)
    at edu.mit.broad.genome.parsers.TxtDatasetParser._parseNoDesc(TxtDatasetParser.java:169)
    at edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:131)
    at edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:87)
    at edu.mit.broad.genome.parsers.ParserFactory.readDatasetTXT(ParserFactory.java:202)
    at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:749)
    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<span class="math-container">$1.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$</span>Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
</code></pre>
<p>Edit:</p>
<p><a href="https://i.sstatic.net/yzSaF.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/yzSaF.png" alt="Here is the first few lines of the table I am using " /></a></p>
<p>I am also using GSEA 3.0. What does not make sense is the other files have the right extensions and are not getting this error, but only this file is failing to upload.</p>
<hr />
<p><a href="https://www.gsea-msigdb.org/gsea/index.jsp" rel="nofollow noreferrer">https://www.gsea-msigdb.org/gsea/index.jsp</a></p>
<p>&quot;Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically
significant, concordant differences between two biological states
(e.g. phenotypes). &quot;</p>

CC BY-SA 4.0
2019-03-15T08:49:34.917Z
Hi there, would you mind sharing a bit more details? What have you tried to resolve your problem? DO you think it's a problem of installation or the file? Note also that you can [edit] your question.
Kamil S Jaron
CC BY-SA 4.0
2019-03-15T09:39:02.760Z
Also perhaps it could be useful to know which version of GSEA are using and how are the first lines from the file (or those around YBL028C )
llrs
CC BY-SA 4.0
2019-03-15T11:09:11.720Z
Please show us an example of the file you are trying to load. It is complaining about `YBL028C`. That looks like a gene/protein name, but the tool is trying to read it as a number. So where do you have `YBL028C` in your data? What is a .chip file?
terdon
CC BY-SA 4.0
2021-04-06T08:09:44.097Z
did you already solve the problem? I also came across the same error when uploading a similar .chip file.
qi wu
<errors><gsea>
I am getting a parsing error when uploading .chip file to GSEA software
# I am getting a parsing error when uploading .chip file to GSEA software

(Asked by: username_0 on 2019-03-15)

I get the following error when I try to load a .chip file to GSEA software. What is the problem?
---- Full Error Message ----
There were errors: ERROR(S) #:1
Parsing trouble
java.lang.NumberFormatException: ...

---- Stack Trace ----
# of exceptions: 1
------For input string: "YBL028C"------
java.lang.NumberFormatException: For input string: "YBL028C"
    at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source)
    at sun.misc.FloatingDecimal.parseFloat(Unknown Source)
    at java.lang.Float.parseFloat(Unknown Source)
    at edu.mit.broad.genome.parsers.TxtDatasetParser._parseNoDesc(TxtDatasetParser.java:169)
    at edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:131)
    at edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:87)
    at edu.mit.broad.genome.parsers.ParserFactory.readDatasetTXT(ParserFactory.java:202)
    at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:749)
    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$1.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

Edit:

I am also using GSEA 3.0. What does not make sense is the other files have the right extensions and are not getting this error, but only this file is failing to upload.

https://www.gsea-msigdb.org/gsea/index.jsp
"Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically
significant, concordant differences between two biological states
(e.g. phenotypes). "

**Tags:** errors, gsea
> **Comments:**
> **username_1**: Hi there, would you mind sharing a bit more details? What have you tried to resolve your problem? DO you think it's a problem of installation or the file? Note also that you can [edit] your question.  
> **username_2**: Also perhaps it could be useful to know which version of GSEA are using and how are the first lines from the file (or those around YBL028C )  
> **username_3**: Please show us an example of the file you are trying to load. It is complaining about `YBL028C`. That looks like a gene/protein name, but the tool is trying to read it as a number. So where do you have `YBL028C` in your data? What is a .chip file?  
> **username_4**: did you already solve the problem? I also came across the same error when uploading a similar .chip file.  

---

## 0 answers

