Error in loading files into the GSEA software
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Entering edit mode
8 weeks ago

Hi everyone

I have some trouble with my RNA-seq file when I try to upload it for analysis with GSEA. I am getting the following error:

Can anyone help me fix it? many thanks!

---- Full Error Message ----
There were errors: ERROR(S) #:1
Parsing trouble
java.lang.IndexOutOfBoundsExcept ...

---- Stack Trace ----
# of exceptions: 1
------Index 0 out of bounds for length 0------
java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0
    at java.base/jdk.internal.util.Preconditions.outOfBounds(Unknown Source)
    at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Unknown Source)
    at java.base/jdk.internal.util.Preconditions.checkIndex(Unknown Source)
    at java.base/java.util.Objects.checkIndex(Unknown Source)
    at java.base/java.util.ArrayList.remove(Unknown Source)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.GctParser._parse(GctParser.java:142)
    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)
GSEA • 104 views
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