Duplicate row name error using Limma

Question: Duplicate row name error using Limma

15 days ago by

Hi, Trying to run limma on Galaxy. After downloading my files, which contain gene IDs, I get these errors:

Fatal error: Exit code 1 () Error in row.names<-.data.frame(*tmp*, value = c("A_07_P000003", "A_07_P000008", : duplicate 'row.names' are not allowed Calls: row.names<- -> row.names<-.data.frame In addition: Warning message: non-unique values when

I shall instead try to run the analysis on RStudio to overcome this problem. But, before that I want to make sure that the problem cannot be solved directly on Galaxy.

Thanks for the help Ignacio

limma galaxy edger • 69 views

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modified 13 days ago by Jennifer Hillman Jackson ♦ 25k • written 15 days ago by ignacio.rangel • 0

14 days ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This tool requires headers in the count files (similar to EdgeR). Featurecounts includes a header. HTseq-count does not (but you could add these in -- see the tool form help for the expected format).

What tool generated the count inputs? Maybe try Featurecounts in Galaxy instead and see if that resolves the problem?

Thanks! Jen, Galaxy team

ADD COMMENT • link written 14 days ago by Jennifer Hillman Jackson ♦ 25k

13 days ago by

ignacio.rangel • 0

ignacio.rangel • 0 wrote:

Hi Jen, Thanks for your answer. However, as I understand Featurecounts is a pipeline for RNA-seq data. What I have is microarray data produced by Agilent. My count files contain headers. So, I assume that should not be the problem. Ignacio

ADD COMMENT • link written 13 days ago by ignacio.rangel • 0

Ok, thanks for explaining.

The headers in your data differ from those on the tool form examples. I would suggest modifying the data columns included and the headers to match the examples to see if that resolves the job error. Many tools are picky about expected input formats/labels.

ADD REPLY • link modified 13 days ago • written 13 days ago by Jennifer Hillman Jackson ♦ 25k

Hej again Jen, Still no joy even after re-shaping my files to mimic the form examples. I am going back to RStudio now and try to solve the problem from there - in case I get the same response-. But thanks for the time and effort. Ignacio

ADD REPLY • link written 13 days ago by ignacio.rangel • 0

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