GSEA rnk-file.

Question

[beginner123]

I have troubles loading my rnk file to GSEA. The error it gives: Does anyone know what to do? I'm kind of lost now.

<Error Details>

---- Full Error Message ----
There were errors: ERROR(S) #:1
Parsing trouble
java.lang.NumberFormatException: ...

---- Stack Trace ----
# of exceptions: 1
------For input string: "lfcSE"------
java.lang.NumberFormatException: For input string: "lfcSE"
    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:555)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:769)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:735)
    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)

Answer 1

[Ming Tommy Tang]

it looks like your input format is not right. it complains about lfcSE. You may remove the header and try it again.

Answer 2

[ATpoint]

Here is how the rnk file must look: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#RNK:_Ranked_list_file_format_.28.2A.rnk.29

lfcSE is a name from DESeq2 results, so you're probably providing the wrong data (format).