EdgeR, DESeq2 not returning main results after analysis



I am trying out deseq2 and edgeR for differential analysis on usegalaxy.org, however, on both occasions, I only get plots (which look very ok) but no actual result files or tables of DEGs as output (shows ‘this list is empty’ instead). Please help, what could be wrong?


Hi - Would you please send an email to galaxy-bugs@lists.galaxyproject.org and include the following:

  • A shared link to the history that contains the unexpected results. How to generate a history share link: Sharing and Publishing your work. Make sure to check the box to share all objects. Unshare and re-share if you have already generated the link and are not sure if objects were shared.
  • Numbers of the datasets with the empty results.
  • A link to this post, so we can link the two.

The galaxy-bugs mailing list is internal to the admins of the Galaxy Main https://usegalaxy.org server and your data will remain private to our team for troubleshooting purposes only. This might be a cluster/server problem, or possibly an input/setting problem.


Thank you for your mail Jennifer. Everything seems to work fine now, surprisingly the tools worked as expected after I repeated the analysis today. I think the problem has been fixed already.



Thanks for letting us know! Perhaps there was some transient cluster issue, now resolved.