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!