ERROR PARSING DATA

[Mr. MOINUDDIN]

Hello,

I am a researcher at CSIR-Central Drug Research Institute, Lucknow, India and for one of my studies I have been using GSEA windows 64-bit application for a year now and performing GSEA analysis on my Transcriptomics data. But, this time I am getting the same error message despite the fact that I am using the same input files that I used for previous analysis.

Expression file is not getting uploaded.

Here is the error message that I am getting:

<Error Details>

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

---- Stack Trace ----
# of exceptions: 1
------Bad format - expect ncols: 2 but found: 14 on line >NAME description Control1 Control2 S-016-1034_1 S-016-1034_2 SCR1 SCR2 Raptor_siRNA1 Raptor_siRNA2 Rictor_siRNA1 Rictor_siRNA2 SCR_siRNA1 SCR_siRNA2<
If this dataset has missing values, use ImputeDataset to fill these in before importing as a Dataset------
edu.mit.broad.genome.parsers.ParserException: Bad format - expect ncols: 2 but found: 14 on line >NAME description Control1 Control2 S-016-1034_1 S-016-1034_2 SCR1 SCR2 Raptor_siRNA1 Raptor_siRNA2 Rictor_siRNA1 Rictor_siRNA2 SCR_siRNA1 SCR_siRNA2<
If this dataset has missing values, use ImputeDataset to fill these in before importing as a Dataset
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.TxtDatasetParser._parseNoDesc(TxtDatasetParser.java:145)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:129)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:86)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readDatasetTXT(ParserFactory.java:201)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:748)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:725)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:51)
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)

The file that I am trying to upload is attached below in.txt format. Please help me with the issue. I have prepared this file myself as I used to prepare earlier. I am not able to figure out what is the mistake that I am committing or there is some software issue. I have also tried uninstalling and reinstalling the software.

Thanks

MOIN

[Anthony Castanza]

Hi Moin,

I took a look at the file you sent to the gsea-team address, it looks like the issue here is that you've used the .txt file extension instead of the .gct extension. The wrong extension has caused GSEA to attempt to read the file using the incorrect parsing method. Changing the file extension to .gct should allow the file to load.

Let me know if you have additional questions after attempting this fix

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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