delivery error

[Pierre Laplante]

Hello,

After running a GSEA, I cannot get the output of the analysis, even though the job is shown to have finished running. An error message is specified at the top, with no details provided.

See the screenshot attached for reference.

I have succesfully run GSEA with other custom .gmt, with the same .gct and .cls, so I don't really know what to do.

Thank you in advance.

Regards,

Pierre Laplante

[Ted Liefeld]

Hi,

the error message reflects an issue in the browser javascript and is not relevant to the job I believe.  it looks like the job did complete on the back end but the GenePattern server is either not seeing it as complete or is failing to retrieve the results.  I am out of the office today with limited connectivity but will try to find the cause once I get back to a computer.  In the meantime you can try rerunning the job.  If that fails as well, let me know and I will manually retrieve the results from the back end and email them to you.

Thanks for your patience,

Ted

[Ted Liefeld]

Hi again,

I don't yet have a fix but the problem seems to be that one or more of the files generated by GSEA have filenames containing characters  that our database is rejecting (SQL error 1366).  Our database is using the latin 1 character encoding.  I think its values such as the beta in 'TGFβ' from your gmt file that is causing the problem.  Try converting your gmt file to use only latin characters and that should fix the issue.  You may need to also check your gct and cls files similarly, but I think the gmt alone is causing the issue since it is the gene set names that are used for filenames, and it is the registration of the filenames that is failing.

Hope this helps

Ted