loading data file into GSEA

Question

[ashkan]

Hi Guys, I am trying to use GSEA (got it from broad institute). I downloaded the software. I got DEGs using edgeR and my file (which is tab-separated or .txt) looks like the small example below: small example:

gene_ID logFC   logCPM  LR  PValue  FDR
ENSG00000000003 0.9401595634851 6.1372543882    32.2921356768863    1.32649126018224e-08    2.17258715481139e-07
ENSG00000000005 7.76297624974972e-16    -2.49752868428905   0   1   1
ENSG00000000419 0.432769218331306   6.29048967094097    7.86686480273069    0.00503488744519358 0.0244714053664738
ENSG00000000457 -0.0301974715116994 3.82577080529457    0.0279829192965257  0.867148985426077   1
ENSG00000000460 -0.225091314245781  4.08050259595373    1.67035993326671    0.196210331309121   0.453720973569106
ENSG00000000938 -3.98356346527839   -1.90061322084491   4.91219642148514    0.0266677094730875  0.0971862849888048

I tried to load my data file to GSEA but did not work. do you guys know how I can resolve this problem?

[WouterDeCoster]

"did not work" -> try to be more precise when describing an error message. What didn't work?

To me this looks like a problem of incompatibility with gene identifiers used by the genesets from GSEA and those in your experiments. However, I think GSEA is well documented and you should be able to find what you need there.

If I check your earlier questions I can trace what analysis you are performing, and every step you turn to us for help. We don't mind helping, but every thing you solve on your own will make you a better (bionformatic) scientist. For most things we also just struggle with until the damn tool works. It can take a few hours, a day or a week, but the reward is far bigger when you finally solve the issue. And the next issue will be easier to solve because of your experience with solving issues :)

[TriS]

here you will find info on what you need to run it... http://software.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html pay attention to the data format, which kind of data they take and which files you need. after you try that out, if it doesn't work, we'll be happy to help troubleshooting :)

Answer 1

[peter.r.flanagan]

HI All,

I am also trying to load a .txt file into GSEA that I have exported from StrandNGS but the file will not import. I have attached the error below. Any help would be great.

Cheers,

Peter

<error details="">

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

---- Stack Trace ----

of exceptions: 1

------For input string: "up"------ java.lang.NumberFormatException: For input string: "up" at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043) at sun.misc.FloatingDecimal.parseFloat(FloatingDecimal.java:122) at java.lang.Float.parseFloat(Float.java:451) 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$1.call(SwingWorker.java:295) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at javax.swing.SwingWorker.run(SwingWorker.java:334) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)