Error loading data

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Tatiana Fonseca

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Jun 21, 2021, 12:38:36 PM6/21/21
to gsea-help
Hello,
I am having issues when I try to load my data to GSEA.  I created my GCT file using the GEOImporter module of the GSE119351 and for the CLS file I used the Clsfile Creator module. I checked the extension of the files and presence of comma but didn't worked. The following error appears:

For GCT:

 

<Error Details>

 

---- Full Error Message ----

There were errors: ERROR(S) #:1

Parsing trouble

java.lang.NumberFormatException: ...

 

---- Stack Trace ----

# of exceptions: 1

------For input string: "NA"------

java.lang.NumberFormatException: For input string: "NA"

                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.GctParser._parseHasDesc(GctParser.java:215)

                at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.GctParser._parse(GctParser.java:167)

                at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.GctParser.parse(GctParser.java:117)

                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:746)

                at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:725)

                at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:51)

                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)

 

 

For the CLS file:

<Error Details>

 

---- Full Error Message ----

There were errors: ERROR(S) #:1

Parsing trouble

java.lang.IllegalArgumentExcepti ...

 

---- Stack Trace ----

# of exceptions: 1

------Class with this name already exists: AMG . The Classes in a Template must be unique------

java.lang.IllegalArgumentException: Class with this name already exists: AMG . The Classes in a Template must be unique

                at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateImpl.add(TemplateImpl.java:219)

                at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateFactory.createTemplate_ordered_assign(TemplateFactory.java:218)

                at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateFactory.createTemplate(TemplateFactory.java:114)

                at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ClsParser._parse_genecluster_style_categorical(ClsParser.java:250)

                at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ClsParser.parse(ClsParser.java:226)

                at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory._readTemplates(ParserFactory.java:341)

                at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readTemplate(ParserFactory.java:292)

                at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:752)

                at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:725)

                at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:51)

                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

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Jun 21, 2021, 1:01:10 PM6/21/21
to gsea...@googlegroups.com
Hi Tatiana,

I replied on the team list to the GCT error, but looks like I missed the CLS error. For that one, it looks like the same phenotype was defined more than once on the second like of the CLS. In the CLS format the second line should be a unique listing of all the phenotypes that could occur in the dataset in the order they first appear. Then the third line should list one of those phenotypes for each sample in the dataset.

Again, let me know if you have any additional questions,

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

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