Cannot get access to gene sets database.

[Alexander Suvorov]

Cannot get access to gene sets database. When select "Gene matrix (from website)" get an error message: 

Error listing Broad website

String index out of range: -16

Choose gene sets from other tabs

This happens with GSEA and GSEAPreranked. Here is the log:

< Process output will appear below >

Jul 17, 2018 12:44:41 PM java.util.prefs.WindowsPreferences <init>

WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0x80000002. Windows RegCreateKeyEx(...) returned error code 5.

Done initing things while splashing

ERROR - java.lang.StringIndexOutOfBoundsException: String index out of range: -16

ERROR - java.lang.StringIndexOutOfBoundsException: String index out of range: -16

ERROR - java.lang.StringIndexOutOfBoundsException: String index out of range: -16

ERROR - java.lang.StringIndexOutOfBoundsException: String index out of range: -16

I have Windows 7 Enterprise, Java V8.

[Helga Thorvaldsdottir]

Hi,

Thanks for letting us know. 

While we investigate, you can download the gene set collections you want to use from the GSEA/MSigDB website, and load them into the GSEA application: 

 - Click on the Downloads tab at www.gsea-msigdb.org;

-  Scroll down and download the .gmt file for the gene set collection(s) you want to use;

 - Load them into the GSEA application in the 'Load data' tab;

 - When setting the parameters for the GSEA run, select the "Gene matrix (local gmx/gmt)" tab in the 'Gene sets database' window (that tab is not visible by default, click on the triangle/arrow to scroll right to see it);

 - Select the local .gmt file(s) you loaded.

Helga

[David Eby]

Hi Alexander,

Some extra files were rolled out as part of yesterday's MSigDB 6.2 release that were causing trouble.  These have been cleaned up and the selectors should be working as normal.

Sorry for any inconvenience.

Regards,

David

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

[Nha Nguyen]

I cannot get access gene sets database. the  errors included: 

• Error listing Broad website
• Connection reset 

• Choose gene sets from other tabs 

how to fix it????

Vào lúc 10:32:25 UTC+8 ngày Thứ Tư, 18 tháng 7, 2018, David Eby đã viết:

[David Eby]

Hi,

Those file listings come from our FTP servers.  Unfortunately, some IT departments block FTP on their local networks which results in this error.  The simplest workaround is listed in Helga's message earlier in the thread.  Quoting from there:

You can download the gene set collections you want to use from the GSEA/MSigDB website, and load them into the GSEA application: 

 - Click on the Downloads tab at www.gsea-msigdb.org;
-  Scroll down and download the .gmt file for the gene set collection(s) you want to use;
 - Load them into the GSEA application in the 'Load data' tab;
 - When setting the parameters for the GSEA run, select the "Gene matrix (local gmx/gmt)" tab in the 'Gene sets database' window (that tab is not visible by default, click on the triangle/arrow to scroll right to see it);
 - Select the local .gmt file(s) you loaded.

Additionally, we provide downloadable ZIP bundles for all the MSigDB files on that same page for those who might need multiple files.

Alternatively, you can also consult with your IT department to see if they are willing to unblock FTP for your computer.

Regards,

David

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

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