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.
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