Unable to load expression data set

[S Reisinger]

Hi,

I am new to GSEA but have been shown how to analyse RNA Seq data and thought everything was pretty clear, including the preparation of an adequate expression data file - but am now failing at this very first step: I can't seem to upload my file in .txt format, the program instead keeps showing the following error:

<Error Details>

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

---- Stack Trace ----
# of exceptions: 1
------For input string: "FAIL"------
java.lang.NumberFormatException: For input string: "FAIL"
    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._parseHasDesc(TxtDatasetParser.java:229)
    at edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:129)
    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)

I am also attaching a screenshot of my txt file for reference... although I followed the instructions on the GSEA / Broad Institute wiki page exactly. Am I missing something?

I have been checking and googling for hours now, and while I don't seem to be the only one with this issue (error when uploading txt files...), the solutions that worked for others do not seem to work here!

I would be grateful for any advice anyone here could give me. Thanks in advance!

Sincerely,

Sonali Reisinger

[David Eby]

Hi Sonali,

There's nothing obviously wrong with the screenshot of data you posted, but here are a few suggestions:

• Be careful about any fields with blank, NA, NaN, or similar values.  How you replace those is up to you; consult a local statistician for advice.  For example, you might consider these as zero-valued, or it might be better to remove the entire row (or column!) depending on the nature of the data.  NA should be fine for the Description as you have it here.
• When working in spreadsheet software like Excel be extremely careful that it doesn't auto-convert any fields (see Zeeberg, et al 2004).  This is less of a problem for numeric data than it is for something like gene symbols  (converting e.g. SEPT1 into a date).

I hope this helps.  We're hoping to improve these error messages in a future release.  Feel free to send the file if you continue having problems.

Regards,

David

David Eby
www.gsea-msigdb.org
igv.org
genepattern.org

[S Reisinger]

Hi David,

Thanks so much for your quick reply, it's much appreciated. I will go through the dataset with your suggestions in mind, hopefully I'll find something. Otherwise I may get back in touch!

Best wishes,

Sonali