Error for input string "DESCRIPTION"

[Felix Dust]

Hello,

I´m trying to perform a GSEA analysis. Unfortunately the software reports an error when creating the expression dataset file. I get the following message:

<Error Details>

 

---- Full Error Message ----

There were errors: ERROR(S) #:1

Parsing trouble

java.lang.NumberFormatException: For input string: "DESCRIPTIO ...

 

---- Stack Trace ----

# of exceptions: 1

------For input string: "DESCRIPTION"------

java.lang.NumberFormatException: For input string: "DESCRIPTION"

         at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(Unknown Source)

         at java.base/jdk.internal.math.FloatingDecimal.parseFloat(Unknown Source)

         at java.base/java.lang.Float.parseFloat(Unknown Source)

         at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.parseStringToFloat(AbstractParser.java:250)

         at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.parseFieldsIntoFloatArray(AbstractParser.java:361)

         at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.parseTextMatrixToDataset(AbstractParser.java:277)

         at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:108)

         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:759)

         at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:736)

         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)

 

 Could you please help me to solve this problem? I have attached the txt-file.
Many thanks!
Felix Dust

[Anthony Castanza]

Hi Felix,

There are a couple small issues with this file that are preventing it from loading. The first is the file extension, this file currently has the .txt extension, but it is formatted as a GCT file, so the file extension will need to be changed to .gct to reflect this data structure. Secondly, your data is using a comma as a decimal separator, unfortunately the GSEA data parser requires the EN-US convention of using a . (period) as the decimal separator.

Finally, the header indicates that there are 21448 genes in the file, however by my count there are only 21433, so the header will need to be changed to reflect this.

After making these three changes the file should load.

Do also note that this file will require you to use the collapse functions with the appropriate Clariom chip file, and due to the sample number will need to be run with the gene_set permutation method.

Please let me know if you have any questions, or encounter additional issues.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Felix Dust]

Hello Anthony,

Thank you very much for your help in creating my expression dataset file. I was able to successfully upload this and the phenotype file.
As you suggested, I selected ‘gene_set’ in the ‘Permutation method’ field.

I am still having problems selecting the appropriate chip platform. My data was generated by Affymetrix Clariom S. Using ‘Human_AFFY_HG_U133’, “Human_AFFY_HG_U95” and ‘Human_AFFY_HuGene’ resulted in an error.

On 9 October 2020, you helped the user ‘Tingting’ with a similar configuration and uploaded a CHIP file  (Human_Clariom_S.r1_MSigDB.7.2_REMAPPED_PATCH.chip) that is compatible with the Clariom platform. I used this and it worked.

My question to you: Is this CHIP file still up to date and can I still use it? Or is there a more recent version that you could provide me with?

Thank you very much!

[Anthony Castanza]

The current version of this chip file for the latest (2025.1) release of MSigDB is available from our repository here: https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations/human/Human_Clariom_S.r1_MSigDB.v2025.1.Hs_REMAPPED_PATCH.chip

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego