Question: How to solve DESeq2 error
gravatar for wangl16
4 months ago by
wangl1610 wrote:

For RNA analysis, I finished TopHat , HTseq-count. But When I run DESeq2 for two groups, error came out. Below is this error "An error occurred with this dataset: Fatal error: An undefined error occurred, please check your input carefully and contact your administrator. Error in row.names<*tmp*, value = value) : duplicate 'row.names' are not allowed"

How can I solve this problem. Thanks!

rna-seq deseq2 open • 388 views
ADD COMMENTlink written 4 months ago by wangl1610

I am having the exact same issue. Even using reference files that have worked previously, I am getting the row.names error upon running DEseq2. The htseq-count files do not have any replicated row names so I am unaware of what else I can do to move forward. Any advice would be appreciated.

ADD REPLYlink written 4 months ago by kkr51690

Hi - I am unable to reproduce this at Galaxy Main If working at that server or can reproduce the problem there, would one of you please send in a bug report? Be sure to leave all inputs/outputs undeleted and include a link to this post so we can connect the two.

I have seen many odd, seemingly unspecific errors come up for this tool when replicates are not input - which are required when using the tool in Galaxy (and line-command, if meaningful results are wanted). There have also been problems with headers in the count files versus the tool form settings used. I can't recall if this specific error came up related to either of those two known usage problems, but looking at an example will clarify what is going on. And if there is a new tool bug, we'll want to fix it.

Thanks! Jen, Galaxy team

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson25k
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