Question: Converting REFSeq IDs to Entrez IDs for KEGG analysis - "geneid of incorrect length"?
gravatar for saw44
10 months ago by
saw4410 wrote:

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!

rna-seq edger kegg deseq R • 338 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 10 months ago by saw4410

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

ADD REPLYlink written 10 months ago by Ashastry60
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1624 users visited in the last hour