error uploading gct file to gsea
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3 months ago

Hello everyone

I'm trying to upload my gct file of the normalized RNAseq counts for mouse into GSEA. I get errors that the last line in my gt file has bad info. I have changed the number of probes in the gct file, also tried deleting the last row, but still gives me error with the last row number having bad info. --- Stack Trace ----

of exceptions: 1

------Gct file with bad row/col info on line: 16313------ edu.mit.broad.genome.parsers.ParserException: Gct file with bad row/col info on line: 16313 at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.GctParser._parse(GctParser.java:130) 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)

Any idea what the issue is?

Thank you

gsea • 287 views
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file with bad row/col info on line: 16313

no?

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