Converting REFSeq IDs to Entrez IDs for KEGG analysis

Converting REFSeq IDs to Entrez IDs for KEGG analysis - "geneid of incorrect length"?

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Entering edit mode

4.5 years ago

saw44 ▴ 30

I have a list of REFSeq IDs from RNA seq and differential expression analysis. I want to run this through KEGG so I can see which pathways are up or down regulated.

For kegga() in R I need to convert these to Entrez IDs. I've used Biomart, but the output that I get has a different number of IDs to my original dataset. So, when I try and run kegga(), I get this error:

Error in kegga.MArrayLM(data, species = "Mm", geneid = gene_list$ID) : 
  geneid of incorrect length

Is this because there are non-coding RNAs in my REFSeq dataset? How can I fix this problem so I can do my pathway analysis?

Answers are greatly appreciated!

R rna-seq kegg deseq edger • 1.3k views

ADD COMMENT • link updated 4.3 years ago by Biostar 20 • written 4.5 years ago by saw44 ▴ 30

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Can you provide more information? Is there any missing value in the ID column?

ADD REPLY • link 4.5 years ago by Ashastry ▴ 60

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