0
$\begingroup$

I've made my files for a GSEA ANALYSIS, but the software gives me this error:

---- Full Error Message ---- There were errors: ERROR(S) #:1 Parsing trouble java.lang.NumberFormatException: ... ---- 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:200) at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:758) 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) 

These are the first lines of my file, made up by 18839 rows of genes:

#1.2 18839 9 NAME description ASPC1 CFPAC1 HS766T BXPC3 CAPAN1 HPAFII PANC0813 PaTu8902 SU8686 A1BG NA 0.13750352 0.15055968 0.16349873 0 0.37851162 0.01435529 0 0.01435529 2.10433666 A1CF NA 3.45285896 0.08406426 0.05658353 0 0.32192809 2.1210154 0.01435529 0 0.04264434 A2M NA 0.07038933 0.20163386 0.48542683 0.21412481 0.05658353 0.04264434 0.20163386 0.05658353 0.15055968 A2ML1 NA 0.01435529 0.01435529 0 1.88752527 0.21412481 0.02856915 2.70708299 2.63459327 0.71369581 A3GALT2 NA 0.02856915 0 0 0 0 0.02856915 0.04264434 0.02856915 0 A4GALT NA 3.46466827 3.36176836 3.09423607 4.22573765 2.50589093 3.61941301 3.21723072 0.01435529 3.34198575 A4GNT NA 0 0 0 0 0 0 0 0.01435529 0.26303441 ``` 
$\endgroup$
1
  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$ Commented May 9, 2024 at 11:58

1 Answer 1

0
$\begingroup$

A similar error has been described in the past and attributed to the presence of missing observations in the data.

Have you checked your data and tried to look for e.g. NA values? It seems that GSEA does not work with missing data.

$\endgroup$

Start asking to get answers

Find the answer to your question by asking.

Ask question

Explore related questions

See similar questions with these tags.