EdgeR duplicate row error

Question: EdgeR duplicate row error

20 days ago by

sudheendrar • 10 wrote:

HI all, I know that there have been previous posts about this error but here is my encounter with it. Is there something specific between HTSEq-Count output to EdgeR?

When I use HTSEQ-output for EdgeR I get following error "Fatal error: Exit code 1 () Error in row.names<-.data.frame(tmp, value = c("X0", "X4", "X4", : duplicate 'row.names' are not allowed Calls: row.names<- -> row.names<-.data.frame Warning message: non-unique values when setting 'row.names': ‘X0’," however, when i use the same HTSEQ-out for DSEQ2 i do not get any errors in addition, if I use featurecount output for EdgeR or DSEQ2, i do not get any errors either. I also tried not using annotation file for EdgeR, i still get that duplicate row name error.

help me out please!

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modified 16 days ago by Jennifer Hillman Jackson ♦ 25k • written 20 days ago by sudheendrar • 10

16 days ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The problem is a missing header line. You can add this in yourself, or use FeatureCounts instead of HTseq-count.

More details in this prior post: https://biostar.usegalaxy.org/p/29403/

Thanks! Jen, Galaxy team

ADD COMMENT • link written 16 days ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen. Any idea why HTSEq2-count output (despite having no header) is compatible with DSEq2 but not EdgeR? Can anything be done with EdgeR wrapper in Galaxy? just asking. I am dealing with dataset collection with a lot of replicates, hence downloading all HTSEq2-count files and adding a header reuploading them! Is there any other way of doing this?

Best wishes.

ADD REPLY • link written 16 days ago by sudheendrar • 10

For your case, I would suggest running the collection through Featurecounts instead of HTseq-count. This is the intended count data to be input to the tool (both are from the same tool authors). For more details, review the help on the EdgeR tool form (scroll down to find it).

Deseq2 has an option to specify whether the data has a header or not. I'm not exactly sure why EdgeR does not have this option but will ask the developers if it would be possible to include it.

ADD REPLY • link modified 15 days ago • written 15 days ago by Jennifer Hillman Jackson ♦ 25k

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