loading data error

[hexin chen]

Dear Sir/Madam,

Could you please tell me what is wrong with my data format?

Thanks a lot!

Hexin

--- Full Error Message ----

There were errors: ERROR(S) #:1

Parsing trouble

java.lang.NumberFormatException: ...

---- Stack Trace ----

# of exceptions: 1

------For input string: "NA"------

java.lang.NumberFormatException: For input string: "NA"

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.GctParser._parseHasDesc(GctParser.java:215)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.GctParser._parse(GctParser.java:167)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.GctParser.parse(GctParser.java:117)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readDatasetGct(ParserFactory.java:159)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readDatasetGct(ParserFactory.java:129)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:746)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:725)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:51)

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 Hexin,

 

The sample of your file that you sent appears fine to me. GSEA however, seems to be finding an “NA” value somewhere in one of the sample’s count values, but it isn’t saying exactly where in the error message which is unusual. I would check carefully for any “NA” strings other than those in the description field.

If you still can’t identify any problems, you can send your full data file to gsea...@broadinstitute.org, we’ll keep it confidential and only use it for debugging.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

http://gsea-msigdb.org/

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[hexin chen]

Hi Anthony,

Thanks a lot for your help! Yes, I founds some "NA' in the data. Should I delete them or replace them with a value?

Hexin

[Anthony Castanza]

Hi Hexin,

 

For RNA-seq data, NA’s is rather surprising, you might want to look back at the raw data and see where they might’ve come from. If they’re zeros in the original data, you should replace with a zero, but if they weren’t expressed I’m not sure why they would’ve been coded as “NA”. More likely they represent outliers or something else that caused them to be rejected by some sort of internal logic in whatever preproccessing you did on the data, in that case you should delete the “NA” (leave a blank cell if, for example, looking at the data in excel). That will cause GSEA to not consider a value for that sample for that gene in the internal differential expression calculation.

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/4dfc527a-7529-4caf-b163-01f8e98c85dbn%40googlegroups.com.

[hexin chen]

Hi Anthony,

Thank you so much! The problem has been solved. 

Hexin