Issue loading RNA-seq data into GSEA desktop application

[Hasse Addinsell]

Hi, 

I've been trying to load my RNA-seq data into GSEA, with no success. I'm using GSEA 4.4.0 (Java 21.0.6; Windows 11 v10.0 amd64). 

Things I have tried are:

- Making sure there are no duplicated entries or special characters in my column names

- Remove rows with duplicated gene names

- Remove rows with missing values using complete.cases() in R. 

- Using gene names instead of ENSEMBL IDs in column 2. 

The error I get is below. Any help would be massively appreciated!

[1779185320250] [SEVERE] Could not parse '"ENSG00000142611"' as a floating point number in row 1 of the data matrix with Name 'PRDM16'.

[1779185320250] [SEVERE] There were errors: ERROR(S) #:1
Parsing trouble
java.lang.NumberFormatException: For input string: "ENSG00000142611"
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.parseStringToFloat(AbstractParser.java:255)
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)

[Anthony Castanza]

Hi Hasse,

Are you sure this dataset is in compliance with our file format guidelines? https://docs.gsea-msigdb.org/#GSEA/Data_Formats/#_top

The error message indicates that it is trying to parse a gene ID as a float which would point to the data matrix not being formatted correctly.

If you're able to supply the dataset, I can take a look. You can do so confidentially by sending it either to me directly, or to gsea...@broadinstitute.org.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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