I would like to use java GSEA software to analyse RNA-Seq FPKM datasets for enriched KEGG pathways. I made .txt gene expression data that could be read by the programme as well as appropriate .cls phenotype file. I downloaded the KEGG gene sets from :
I use gene symbols in both gene sets and expression table. Unfortunately the analysis comes up with an error message like this:
---- Full Error Message ---- col:4 > matrix's fColCnt:4 ---- Stack Trace ---- # of exceptions: 1 ------col:4 > matrix's fColCnt:4------ java.lang.ArrayIndexOutOfBoundsException: col:4 > matrix's fColCnt:4 at edu.mit.broad.genome.math.Matrix.getColumnV(EIKM) at edu.mit.broad.genome.objects.DefaultDataset.getColumn(EIKM) at edu.mit.broad.genome.objects.TemplateFactory.extract(EIKM) at edu.mit.broad.genome.alg.DatasetGenerators.extract(EIKM) at edu.mit.broad.genome.alg.DatasetGenerators.extract(EIKM) at xtools.gsea.AbstractGsea2Tool.execute_one(EIKM) at xtools.gsea.AbstractGsea2Tool.execute_one_with_reporting(EIKM) at xtools.gsea.Gsea.execute(EIKM) at edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(EIKM) at java.lang.Thread.run(Unknown Source)
I tried many things to fix this problem. I re-run the analysis with number of permutations 1 and 5. I modified the expression file and substituted every value of 0 into 0.001 (I thought that may have been the problem). But it didn't work.
Your help will be deeply appreciated.