Known Issues

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GSEA ftp site unavailable

Problem: When you try to access the CHIP annotation files or the Gene Set Database / MSigDB Browser, you see a connection error.

Solution:

1. Download this large zip file to your local file system.
2. Expand the ZIP file with WinZIP. The file contains all annotation files and gene sets. It also contains the MSigDB XML file, which you will not need.
3. Start GSEA.
4. In GSEA, turn off the internet connection mode. Click Options>Preferences. On the General preferences page, clear the 'Connect over the Internet' option and click OK.
5. Use the Load Data page to load the local annotation files and gen set files.
6. On the Run GSEA page, select the local annotation files and gene set files rather than using the files from the GSEA website.

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GSEA version 2.0.1

GSEA and Snow Leopard

Problem: GSEA does not run under Snow Leopard.

Cause: GSEA currently runs on Mac OS X 10.5.4 (Leopard), but not on Mac OS X 10.6 (Snow Leopard). The GSEA developers are working on the problem.

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GSEA version 2

OutOfMemoryError when running GSEA

Problem: When running an analysis in GSEA. the following error occurs:

---- Stack Trace ----

1. of exceptions: 1
   

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Java heap space------
java.lang.OutOfMemoryError: Java heap space

Cause: The error is either due to improper memory allocation, or because you have reached the limits on your machine.

Solutions:

1. Start GSEA by clicking the Launch button on the Downloads page of the GSEA web site.
2. Run GSEA on a more powerful computer.
3. Use no more than 1,000 permutations.
4. First, collapse gene identifiers to symbols using Chip2Chip tool, then run GSEA on the collapsed data set.
   When running GSEA on the collapsed dataset, make sure that 'Collapse dataset(s)' = false
5. When running GSEA from the command line, use the -Xmx option to specify sufficient maximum amount of memory for the program.

 

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Error in memory.size when running GSEA-R

Problem: When running the example programs provided for R, the following error occurs:

[1] " *** Running GSEA Analysis..."
Error in memory.size(size) : don't be silly!: your machine has a 4Gb address limit

Cause: This is produced by the following line early in the GSEA.1.R file:

memory.limit(6000000000)

This line set the memory limit to a large size as a work around to a platform problem with an earlier R version.

Solution: The easiest fix is just to comment out that line:

# memory.limit(6000000000)

This will allocate the default amount of memory. If after this change the program runs out of memory, change the line to:

memory.limit(max. size in Mbytes available)

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Warning ('\%' is an unrecognized escape) when running GSEA-R

Problem: When running the example programs provided for R, the following warnings occur:

1: '\%' is an unrecognized escape in a character string
2: unrecognized escape removed from "Tag \%"
3: '\%' is an unrecognized escape in a character string
4: unrecognized escape removed from "Gene \%"
5: '\%' is an unrecognized escape in a character string
6: unrecognized escape removed from "\%"
7: '\%' is an unrecognized escape in a character string
8: unrecognized escape removed from " \%)"
9: '\.' is an unrecognized escape in a character string
10: '\.' is an unrecognized escape in a character string
11: unrecognized escapes removed from "\.report\."
12: '\.' is an unrecognized escape in a character string
13: '\.' is an unrecognized escape in a character string
14: unrecognized escapes removed from "\.report\."
15: '\.' is an unrecognized escape in a character string
16: unrecognized escape removed from "\."

Solution: You can ignore these warning messages. They occur when you have R version 2.5 and higher installed.

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Firewall / FTP connection issues for CHIP annotations or Gene Set Databases

Problem: When you try to access the CHIP annotation files or the Gene Set Database / MSigDB Browser, you see an error to the effect:

"Error listing Broad website//  Connection reset//"

Cause: This is probably because you are behind a network firewall or someother network configuration that prevents you from accessing FTP servers on port 500. The Broad chip files and gene sets are placed on a publically accessible Broad FTP server. The GSEA Java Desktop program tries to access the Broad FTP site to provide you easy access to the files but the network configuration blocks access.

Solutions:

1. See if you can temporarily disable your firewall when using GSEA.
2. Consult with your local network administrator to see if they have any suggestions or prior experience such issues.
3. Download the .CHIP, GeneSet databases and MSigDB XML files to your local file system as follows:
   1. Download this large zip file to your local file system.
   2. Expand the ZIP file with WinZIP. The file contains all annotation files and gene sets. It also contains the MSigDB XML file, which you will not need.
   3. Start GSEA.
   4. In GSEA, turn off the internet connection mode. Click Options>Preferences. On the General preferences page, clear the 'Connect over the Internet' option and click OK.
   5. Use the Load Data page to load the local annotation files and gen set files.
   6. On the Run GSEA page, select the local annotation files and gene set files rather than using the files from the GSEA website.

This large ZIP file contains ALL current (as of April 8, 2008) .CHIP annotations, GENE_SET databases and MSigDB.xml file.

 

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Error running leading edge analysis

Problem: When you select a report for leading edge analysis, the following error sometimes occurs:

                   java.lang.NullPointerException
at org.genepattern.gsea.LeadingEdgeWidget.setData(EIKM)
at xapps.gsea.LeadingEdgeReportWidget.setData(EIKM)
at xapps.gsea.LeadingEdgeReportWidget$1.run(EIKM)
at java.lang.Thread.run(Unknown Source)

Solution: Corrected in GSEA v2.0.1.

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"No probe called" error in log while running GSEA

Problem: When you run GSEA, sometimes the following errors appear in the log file:

ERROR - No Probe called: USP9X /// USP9Y on this chip (chip name is >GENE_SYMBOL<)
ERROR - Turning off subsequent error notifications

Solution: You can ignore these errors. The three slashes (///) indicate that the chip file contains ambiguous mappings, typical for Affymetrix notation, where a probe set on the chip cannot be mapped to exactly one HUGO gene symbol. GSEA displays this error and ignores such ambigous probes.

 

GSEA version 1

java.lang.OutOfMemoryError (GSEA v1)

Problem: On the Mac, you can run GSEA from the command line, but when you attempt to use the GSEA application from the desktop you receive errors similar to the following:

---- Full Error Message ----
na

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Stack Trace ----

1. of exceptions: 1
   

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null------

java.lang.OutOfMemoryError

Solution: Corrected in GSEA v2. In GSEA v1, this is a memory issue with the gsea installer on the Mac. As a workaround, use the following command to launch the GSEA application rather than double clicking the icon:

java -Xmx1800m xapps.gsea.Main

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java.lang.NullPointerException (GSEA v1)

Problem: By default, a gene set enrichment analysis uses phenotype permutations. If you have too few samples for phenotype permutation, the following error occurs:

---- Stack Trace ----

1. of exceptions: 1
   

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null------

java.lang.NullPointerException
    at edu.mit.broad.genome.alg.DatasetStatsCore.calc2ClassCategoricalMetricMarkerScores(DatasetStatsCore.java:236)
    at edu.mit.broad.genome.alg.markers.PermutationTestBuilder.<init>(PermutationTestBuilder.java:94)
    at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate_canned_templates(KSTests.java:360)
    at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate(KSTests.java:291)
    at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:156)
    at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:130)
    at xtools.gsea.AbstractGsea2Tool.execute_one(AbstractGsea2Tool.java:103)
    at xtools.gsea.AbstractGsea2Tool.execute_one_with_reporting(AbstractGsea2Tool.java:137)
    at xtools.gsea.Gsea.execute(Gsea.java:111)
    at edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:468)
    at java.lang.Thread.run(Unknown Source)

Solution: Corrected in GSEA v2. In GSEA v1, use gene_set permutation rather than phenotype permutation. For more information, see the description of the Permutation type parameter on the Run GSEA Page in the GSEA User Guide.

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GSEA on Linux

Browser links do not work under Linux

Problem: When running the GSEA desktop application under Linux, buttons and links that would normally open a browser window do not open the browser window.

Work-around: After running an analysis, you cannot click on the Success link to display the result. However, you can go to the directory that contains the analysis report output and open the index.html file in that directory.