GSEA run with just RNK file

Question

[dew]

Dear guys,

May I know if GSEA soft can run with only input file RNK file? When using the client, loading the RNK file, it shows a JAVA error. The file is already Tab-delimited, the first column is gene name, second is the FoldChange.

Thanks a lot!

[Shraddha]

Do you mean that you don't provide a .gmt file? If so, there's no reference and GSEA won't run. It may also be useful for you to show the error message you get.

[dew]

Thanks, it do have a gmt file as a reference. while the first step to load input, it shows error.

java.lang.NumberFormatException: For input string: "fc"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.RankedListParser.parse(RankedListParser.java:72)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readRankedList(ParserFactory.java:556)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:771)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:737)
    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)

[dew]

There were errors: ERRORS #1 Parsing trouble java.lang.NumberFormattException:...

[jv]

Can you provide the command that you used to run GSEA and the first few lines of your RNK file? It make also help to review the GSEA txt format description at https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#TXT:_Text_file_format_for_expression_dataset_.28.2A.txt.29

[dew]

Thanks a lot!

#1  
KLF15   1,09
OR1C1   1,49
C6orf52 -0,89
XKRX    1,43
OXCT2   1,88
RPL17-C18orf32  -1,02
FBXL15  -1,68
FHL1    1,05
NR3C2   1,02
ACP3    1,32
RHOXF1P1    0,88
OR5H14  0,9

I used the GSEA app to load the data, so no command lines.

Thank you very much!

[jv]

Not sure if you are still looking for assistance with this error, but according to the GSEA documentation you should have a DESCRIPTION column (can be blank or filled with NA's) as your second column, after the gene name and before the expression data:

There is one line for each gene. Each line contains the gene name, gene description, and a value for each sample in the dataset.