EdgeR, DESeq2 not returning main results after analysis


#1

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?


#2

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.


#3

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.

Regards,


#4

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