Error in loading my file in GSEA

[Léa Chevalier]

Hi everyone,

I'm having trouble on loading my file on GSEA. I would like to use "GCT: Gene Cluster Text file format (*.gct)" and I followed the instructions on your website to construct my data file.

When I'm loading my data file on GSEA, I have : 

<Error Details>

---- Full Error Message ----
There were errors: ERROR(S) #:1
Parsing trouble
edu.mit.broad.genome.parsers.Par ...

---- Stack Trace ----
# of exceptions: 1
------Column not found: Probe Set ID------
edu.mit.broad.genome.parsers.ParserException: Column not found: Probe Set ID
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.indexOf(AbstractParser.java:510)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ChipParser.parse(ChipParser.java:100)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readChip(ParserFactory.java:521)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:779)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:735)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:53)
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)

Can someone help me on this ? 

Thank you 

[Anthony Castanza]

Hi Léa,

Based on the error message, GSEA is either trying to parse this as a CHIP file instead of a GCT file, or it is also trying to parse a chip file and failing on that and not this file. Are you by chance trying to load any other files at the same time?
Based on the screenshot you provided this would appear to be Mouse (or Rat) gene symbols data, we offer several chip files for using these species of symbols in various ways so you shouldn't need to load your own (typically, if you have any questions about which chip to use please feel free to reach out).
If you're not loading in a chip file as well could you please double check your file extension and ensure that it is actually .gct and not .chip?
If it isn't either of these things, please let me know.

Additionally, I see you only have 137 genes defined in the file header you provided. Generally GSEA would expect expression data for all expressed genes, and not (for example) just the genes that were found to be significant by differential expression analysis. Do you by chance have a more complete dataset? You're very likely to encounter significant issues attempting GSEA with these few genes.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

--
You received this message because you are subscribed to the Google Groups "gsea-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gsea-help+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/cc49892d-0265-491b-b9b3-77f564872772n%40googlegroups.com.

[Léa Chevalier]

Hi,

Thank you for your response. I'm not using chip file and I was loading my data file as .txt. I don't know how to convert my file into .gct. Can you explain to me how to do it ?
Thank you for your advice about my file, I will complete my data file with all genes.

[Anthony Castanza]

That is quite odd because the error message is definitely referring to the CHIP parser.

As to your file, generally the formatting looks fine for a GCT file, it just needs to be saved out of excel as Tab Delimited Text (.txt), then the .txt file extension needs to be changed to .gct

If you're still having trouble, you can send us the file confidentially at gsea...@broadinstitute.org and I can try to debug the issue more directly.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/12249e5f-1365-43f4-8763-c33f3b93fa56n%40googlegroups.com.