<p>I built the matrix as the gmt example in <a href="https://docs.gsea-msigdb.org/#GSEA/Data_Formats/" rel="nofollow noreferrer">https://docs.gsea-msigdb.org/#GSEA/Data_Formats/</a> but It still has errors when I try to run it.
When I try the gene set from <a href="https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/HALLMARK_ADIPOGENESIS.html" rel="nofollow noreferrer">https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/HALLMARK_ADIPOGENESIS.html</a>
in .gmt format and load it with GSEA appears this error:</p>
<p>Thank you so much</p>
<p>Nerea</p>
<pre><code>
---- Full Error Message ----
col:34 &gt; matrix's fColCnt:34

---- Stack Trace ----
# of exceptions: 1
------col:34 &gt; matrix's fColCnt:34------
java.lang.ArrayIndexOutOfBoundsException: col:34 &gt; matrix's fColCnt:34
at org.gsea_msigdb.gsea/edu.mit.broad.genome.math.Matrix.getColumnV(Matrix.java:261)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.DefaultDataset.getColumn(DefaultDataset.java:289)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateFactory.extract(TemplateFactory.java:85)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.alg.DatasetGenerators.extract(DatasetGenerators.java:292)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.alg.DatasetGenerators.extract(DatasetGenerators.java:288)
at org.gsea_msigdb.gsea/xtools.gsea.AbstractGsea2Tool.execute_one(AbstractGsea2Tool.java:79)
at org.gsea_msigdb.gsea/xtools.gsea.AbstractGsea2Tool.execute_one_with_reporting(AbstractGsea2Tool.java:103)
at org.gsea_msigdb.gsea/xtools.gsea.Gsea.execute(Gsea.java:166)
at org.gsea_msigdb.gsea/edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:391)
at java.base/java.lang.Thread.run(Unknown Source)


</code></pre>

CC BY-SA 4.0
2023-06-20T12:07:17.047Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Community
CC BY-SA 4.0
2023-06-20T22:11:44.250Z
Please show the first few lines of your input file; from the error, this looks like it might be a formatting issue, and without more information about the format of your file we can't help out.
gringer
CC BY-SA 4.0
2023-06-21T13:07:13.980Z
Hello It was a formatting issue. Sorry, I solved the problem. Thank you
Nerea Herrera
CC BY-SA 4.0
2023-06-25T14:26:21.587Z
Great! glad it's resolved. Could you kindly add your resolution as an answer please? Firstly it helps the site because unresolved question continue to circulate, secondly it helps your reputation on the site. This is useful should you wish to ask another question here in the future.
M__
<gsea><errors>
Run gmt format download from GSEA
# Run gmt format download from GSEA

(Asked by: username_0 on 2023-06-20)

I built the matrix as the gmt example in https://docs.gsea-msigdb.org/#GSEA/Data_Formats/ but It still has errors when I try to run it.
When I try the gene set from https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/HALLMARK_ADIPOGENESIS.html
in .gmt format and load it with GSEA appears this error:
Thank you so much
Nerea

---- Full Error Message ----
col:34 > matrix's fColCnt:34

---- Stack Trace ----
# of exceptions: 1
------col:34 > matrix's fColCnt:34------
java.lang.ArrayIndexOutOfBoundsException: col:34 > matrix's fColCnt:34
at org.gsea_msigdb.gsea/edu.mit.broad.genome.math.Matrix.getColumnV(Matrix.java:261)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.DefaultDataset.getColumn(DefaultDataset.java:289)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateFactory.extract(TemplateFactory.java:85)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.alg.DatasetGenerators.extract(DatasetGenerators.java:292)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.alg.DatasetGenerators.extract(DatasetGenerators.java:288)
at org.gsea_msigdb.gsea/xtools.gsea.AbstractGsea2Tool.execute_one(AbstractGsea2Tool.java:79)
at org.gsea_msigdb.gsea/xtools.gsea.AbstractGsea2Tool.execute_one_with_reporting(AbstractGsea2Tool.java:103)
at org.gsea_msigdb.gsea/xtools.gsea.Gsea.execute(Gsea.java:166)
at org.gsea_msigdb.gsea/edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:391)
at java.base/java.lang.Thread.run(Unknown Source)

**Tags:** gsea, errors
> **Comments:**
> **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
> **username_2**: Please show the first few lines of your input file; from the error, this looks like it might be a formatting issue, and without more information about the format of your file we can't help out.  
> **username_0**: Hello It was a formatting issue. Sorry, I solved the problem. Thank you  
> **username_3**: Great! glad it's resolved. Could you kindly add your resolution as an answer please? Firstly it helps the site because unresolved question continue to circulate, secondly it helps your reputation on the site. This is useful should you wish to ask another question here in the future.  

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## 0 answers

