edgeR Reading Error

Question: edgeR Reading Error

10 weeks ago by

mbt • 0

mbt • 0 wrote:

Hi Jennifer?

Still having problems with edgeR. I was able to get DeSeq2 to work by using very simple names for factor name and levels. This does not work for edgeR. I still get the following error error An error occurred with this dataset: Fatal error: Exit code 1 () Error in row.names<-.data.frame(*tmp*, value = c("X0", "X0", "X0", : duplicate 'row.names' are not allowed Calls: row.names<- -> row.names<-.data.frame Warning message: non-unique value when setting 'row.names': ‘X0’

Seems like a data format error. Is it the header? Or is it some data line in the file that it doesn't like?

BTW: I greatly appreciate all your help in getting to this point in the analysis. Thank you for your quick responses and very helpful comments.

Mike

rna-seq • 158 views

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modified 10 weeks ago by mblue9 • 140 • written 10 weeks ago by mbt • 0

10 weeks ago by

mblue9 • 140

mblue9 • 140 wrote:

I think it's the missing header that's causing the issue for you, HTSeq doesn't output one. So you can either manually add a header row with the sample ids to the counts files you have, or use featureCounts instead of HTSeq as that will output a header row and should work fine with edgeR.

ADD COMMENT • link written 10 weeks ago by mblue9 • 140

Thank you! I learned something new, too, about EdgeR! Will add this to the troubleshooting FAQ. :) Jen

ADD REPLY • link written 10 weeks ago by Jennifer Hillman Jackson ♦ 25k

10 weeks ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

You can try troubleshooting on your own first by reviewing the Galaxy tutorials that include this tool and by making sure the inputs match what is expected. Without seeing your analysis it is difficult to guess what else might be going wrong (sorry!).

Galaxy tutorials: https://galaxyproject.org/learn/
Galaxy FAQs (including input data troubleshooting): https://galaxyproject.org/learn/
- My job ended with an error. What can I do? https://galaxyproject.org/support/tool-error/

If you still cannot find the problem after reviewing the above:

If can reproduce the error at Galaxy Main https://usegalaxy.org, a bug report can be sent in from one of the error datasets. Please include a link to this post.
If working at another public usegalaxy.* Galaxy server, you could generate a history share link and post that back here for review (public) or send an email with it directly to galaxy-bugs@lists.galaxyproject.org (private). Note that all inputs/outputs need to be left undeleted and in the same history. Please include a link to this post.
If working at some other public Galaxy server, try contacting the administrators/support at that server (each is independently administered). There might be a known server-specific tool issue of some type.

There could be a tool bug, although every other time I have seen this come up there was a problem with the inputs. Examples: the same input entered more than once; poorly formatted labels; an inconsistent number of replicates entered between factors/factor levels; count files accidentally generated using different reference data (genome and/or annotation)

Thanks! Jen, Galaxy team

ADD COMMENT • link written 10 weeks ago by Jennifer Hillman Jackson ♦ 25k

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