error in uploading the signal file

[Aga gad]

Good day, 

I am trying to load my signal expression file, the following error appears, this is my first time to use GSEA. please guide me how to solve this problem, attached you can find the file i am trying to upload. 

<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: 15 on line >Name Description 2 3 5 7 8 9 10 12 13 16 17 18 19<

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: 15 on line >Name Description 2 3 5 7 8 9 10 12 13 16 17 18 19<

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)

[Anthony Castanza]

Hello,

 

It looks like GSEA is not parsing your dataset properly. It appears to be loading in the file using the parser for .TXT files which need to be formatted to this specification: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#TXT:_Text_file_format_for_expression_dataset_.28.2A.txt.29

 

I would suspect based on the error that this file was formatted as a GCT file: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GCT:_Gene_Cluster_Text_file_format_.28.2A.gct.29

But the file extension wasn't changed from .txt to .gct.

 

If checking the data format and file extension and making sure that they match the appropriate specification doesn't resolve your issue please let us know and we can take a closer look at the data files and see what might be going wrong.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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