Errors: <Error Details> ---- 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.NumberFormatExc
Misha Fotovati
---- 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:250)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.parseFieldsIntoFloatArray(AbstractParser.java:361)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.parseTextMatrixToDataset(AbstractParser.java:277)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:108)
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:53)
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)
Anthony Castanza
Hello,
It appears that this data file is using the .txt file extension but the data is structured as the .gct format. You’ll need to change the file extension to reflect the .gct structure, then GSEA should be able to parse the file correctly.
Let me know if you still have issues after making this change
-Anthony
Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego
From:
gsea...@googlegroups.com <gsea...@googlegroups.com> on behalf of Misha Fotovati <mishaf...@gmail.com>
Date: Tuesday, July 5, 2022 at 11:00 AM
To: gsea-help <gsea...@googlegroups.com>
Subject: [gsea-help] Errors: <Error Details> ---- 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.Numbe...
Hello!
I am having trouble with loading my data on GSEA. To my knowledge I have followed the formatting guidelines so I am not sure why I am recieving this message
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Anthony Castanza
Hello,
What did you change with the file name here? It appears that you’ve given the phenotype label file the “gct” extension, this is the extension for the expression dataset, the phenotype data should be given the “cls” file extension. If you rename the file PhenotypeLabelsmeta.cls it should work. Does it not?
-Anthony
Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego
From: gsea...@googlegroups.com <gsea...@googlegroups.com> on behalf of Misha Fotovati <mishaf...@gmail.com>
Date: Tuesday, July 5, 2022 at 11:24 AM
To: gsea-help <gsea...@googlegroups.com>
Subject: Re: [gsea-help] Errors: <Error Details> ---- 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.N
Hi! Thank you so much that fixed it. I assumed this was also a problem with my phenotypes label file, but even after changing that file name I receive a new error message now:
There were errors: ERROR(S) #:1
Parsing trouble
edu.mit.broad.genome.parsers.Par ...
---- Stack Trace ----
# of exceptions: 1
------Gct file with bad row/col info on line 2: 44 2 1------
edu.mit.broad.genome.parsers.ParserException: Gct file with bad row/col info on line 2: 44 2 1
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.GctParser.parse(GctParser.java:109)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readDatasetGct(ParserFactory.java:159)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readDatasetGct(ParserFactory.java:129)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:758)
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:53)
at java.desktop/javax.swing.SwingWorker$1.call(Unknown Source)
On Tuesday, July 5, 2022 at 2:02:11 PM UTC-4 Anthony Castanza wrote:
Hello,
It appears that this data file is using the .txt file extension but the data is structured as the .gct format. You’ll need to change the file extension to reflect the .gct structure, then GSEA should be able to parse the file correctly.
Let me know if you still have issues after making this change
-Anthony
Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego
From: gsea...@googlegroups.com <gsea...@googlegroups.com> on behalf of Misha Fotovati <mishaf...@gmail.com>
Date: Tuesday, July 5, 2022 at 11:00 AM
To: gsea-help <gsea...@googlegroups.com>
Subject: [gsea-help] Errors: <Error Details> ---- 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.Numbe...Hello!
I am having trouble with loading my data on GSEA. To my knowledge I have followed the formatting guidelines so I am not sure why I am recieving this message
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/0c912d43-c6aa-435a-9f1b-15993237242dn%40googlegroups.com.