GSEA Error Message - "Dataset not set"

Question

[aditi.qamra]

Hi,

I am trying to run GSEA or the first time using the GUI application.

I created all files in the formats specified and they successfully got loaded however on running the command, it gives me an error saying -

---- Full Error Message ----
Dataset not set!!**

---- Stack Trace ----
# of exceptions: 1
------Dataset not set!!------
java.lang.IllegalArgumentException: Dataset not set!!
    at edu.mit.broad.genome.objects.TemplateImplFromSampleNames._ct(EIKM)
    at edu.mit.broad.genome.objects.TemplateImplFromSampleNames.getClass(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)

The command line is -

java -Xmx512m \
  xtools.gsea.Gsea \
  -res C:\Documents and Settings\qamraa99\My Documents\survival\eset.gct.txt -cls \
  C:\Documents and Settings\qamraa99\gsea_home\output\sep29\Normals_vs_Tumors.cls#Tumors_versus_Normals \
  -gmx C:\Documents and Settings\qamraa99\My Documents\survival\stat3_genelists.gmx.txt \
  -collapse false \
  -mode Max_probe \
  -norm meandiv \
  -nperm 1000 \
  -permute gene_set \
  -rnd_type no_balance \
  -scoring_scheme weighted \
  -rpt_label my_analysis \
  -metric Signal2Noise \
  -sort real \
  -order descending \
  -include_only_symbols true \
  -make_sets true \
  -median true \
  -num 100 \
  -plot_top_x 20 \
  -rnd_seed timestamp \
  -save_rnd_lists false \
  -set_max 500 \
  -set_min 15 \
  -zip_report false \
  -out C:\Documents and Settings\qamraa99\gsea_home\output\sep29 \
  -gui false

I really can't seem to figure what's going wrong. Can anybody help ?

Thanks !

Aditi

[bengtpg]

I am having a parsing error problem when loading files into GSEA. According to their documentations it is an extension error. The extensions are fully showing in my Windows 8 system and making sure that phenotype extension is .cls still creates the parsing error. As your problem seems to be similar to mine, could you give me any advice to solve it?

[aditi.qamra]

My problem was not really this but I'd sugeest you save the documents in the exact manner it has been mentioned in the documentation. follow it to the tee. I do remember vaguely not following it completely and running into some issues. If you still run into issues, try mailing the gsea mailing list, they usually do respond back.

Answer 1

[aditi.qamra]

So I figured this on my own - I was creating the phenotype on the fly in the windows GUI and for some reason that was creating this issue. Once I created the phenotype as .cls file and uploaded that, I did not encounter any error. Seems like this bug should be resolved from GSEA's end.

However now if anybody encounters this error - they know what to do !