error 1

[Aracelly Quiroz]

Hello, 

I have been trying to load my gct file to run a standard GSEA. I'm using GSEA v 4.1.0. I made sure the format is right (i.e. its txt delimited and gct file formats) I've already seen the tutorial videos. I tried to go through the conversations available here to see if anyone else encountered the same issue and found one. But they had different error #1. I'm attaching the error message I get when I try to load my file. Please let me know if you would like me to send you the excel file (confidential). 

Thanks, 

Aracelly

<Error Details>

---- Full Error Message ----

There were errors: ERROR(S) #:1

Parsing trouble

java.lang.NumberFormatException: ...

---- Stack Trace ----

# of exceptions: 1

------multiple points------

java.lang.NumberFormatException: multiple points

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)

[Anthony Castanza]

Hi Aracelly,

 

From this error message it would appear that one of the cells in your dataset contains the value “…” it’s unclear if this is the value by itself, or if it’s part of a number (eg: 1…23), this is causing GSEA to fail when reading the file as that multiple decimals can’t be parsed as a numerical value. If you’re unable to identify where this value (or values) occur, you can confidentially send your file to gsea...@broadinstitute.org and we can take a look.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

http://gsea-msigdb.org/

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