GSEA error message help: Empty Gene Line
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5 months ago
Genosa ▴ 140

edu.mit.broad.genome.parsers.ParserException: Empty gene line: <!DOCTYPE html> at row: 0 at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.GmtParser.parse(GmtParser.java:104) at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readGeneSetMatrixT(ParserFactory.java:705) 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:799) at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:787) at org.gsea_msigdb.gsea/xtools.api.param.GeneSetMatrixMultiChooserParam._getObjects(GeneSetMatrixMultiChooserParam.java:122) at org.gsea_msigdb.gsea/xtools.api.param.GeneSetMatrixMultiChooserParam._getGeneSets(GeneSetMatrixMultiChooserParam.java:166) at org.gsea_msigdb.gsea/xtools.api.param.GeneSetMatrixMultiChooserParam.getGeneSetMatrixCombo(GeneSetMatrixMultiChooserParam.java:61) at org.gsea_msigdb.gsea/xtools.gsea.Gsea.execute(Gsea.java:156) at org.gsea_msigdb.gsea/xtools.api.AbstractTool.module_main(AbstractTool.java:417) at org.gsea_msigdb.gsea/org.genepattern.modules.GseaWrapper.main(GseaWrapper.java:287) at org.gsea_msigdb.gsea/xapps.gsea.CLI.main(CLI.java:29)"

I am using GSEA to do some data analysis (online version GenePattern) and I have been constantly stuck at this Empty gene line: <!DOCTYPE html> at row: 0 error message. What does this actually mean? The GCT file, CLS file, geneset database gmt file (I'm using BTM) are all uploaded. Hence I am not sure what has gone wrong.

This is the snippet of the GCT file:

#1.2
22479   3
Gene    Gene Title  d1_fc   d3_fc   d7_fc
IGHM    NA  1.15955 1.10151 3.06971

This is the CLS file format:

#numeric
#timepoint
1 3 7 

Thank you for your help and suggestions.

GenePattern GSEA • 170 views
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