Hi, all!
While I was trying to convert Ensembl ID to Entrez ID using 'mapIDs', I noticed number of missing IDs in the result.
18,453 Ensembl IDs were input, but only 18,364 Entrez IDs were returned.
I was expecting the missing IDs would be presented as 'NA' or something like that. Instead, they weren't included in the result at all.
The data I'm trying to convert IDs,
> head(de)
p_val avg_logFC pct.1 pct.2 p_val_adj fcsign logP metric
ENSMUSG00000000184 0 1.5573130 0.992 0.016 0 1 0 0
ENSMUSG00000053030 0 1.3555568 1.000 0.005 0 1 0 0
ENSMUSG00000037820 0 1.1589184 0.875 0.009 0 1 0 0
ENSMUSG00000005087 0 0.9234463 0.842 0.002 0 1 0 0
ENSMUSG00000026586 0 0.7931385 0.658 0.000 0 1 0 0
ENSMUSG00000050010 0 0.7784591 0.733 0.000 0 1 0 0
and R code I used,
ranks$entrez = mapIds(org.Mm.eg.db,
keys=row.names(de),
column="ENTREZID",
keytype="ENSEMBL",
multiVals="filter")
What seems to be the problem here?
Please, help me!
Thank you!
Thank you for reply! So you're saying is that Ensembl has multiple ID for a Entrez annotation? Am I understanding right? Then how would you handle those situations?
No, I meant to say some genomic features only has an annotation only in Ensembl database , not in Entrez.