I get the following error when I try to load a .chip file to GSEA software. What is the problem?
---- Full Error Message ----
There were errors: ERROR(S) #:1
Parsing trouble
java.lang.NumberFormatException: ...
---- Stack Trace ----
# of exceptions: 1
------For input string: "YBL028C"------
java.lang.NumberFormatException: For input string: "YBL028C"
at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source)
at sun.misc.FloatingDecimal.parseFloat(Unknown Source)
at java.lang.Float.parseFloat(Unknown Source)
at edu.mit.broad.genome.parsers.TxtDatasetParser._parseNoDesc(TxtDatasetParser.java:169)
at edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:131)
at edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:87)
at edu.mit.broad.genome.parsers.ParserFactory.readDatasetTXT(ParserFactory.java:202)
at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:749)
at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:726)
at edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:52)
at javax.swing.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at javax.swing.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Edit:
I am also using GSEA 3.0. What does not make sense is the other files have the right extensions and are not getting this error, but only this file is failing to upload.
https://www.gsea-msigdb.org/gsea/index.jsp
"Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). "
YBL028C
. That looks like a gene/protein name, but the tool is trying to read it as a number. So where do you haveYBL028C
in your data? What is a .chip file? $\endgroup$