Question: mapIDs (AnnotationDBi) returns shorter list of IDs than input IDs
0
gravatar for mbk0asis
12 weeks ago by
mbk0asis530
Korea, Republic Of
mbk0asis530 wrote:

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!

mapids R annotationdbi • 128 views
ADD COMMENTlink written 12 weeks ago by mbk0asis530
2
gravatar for Arup Ghosh
12 weeks ago by
Arup Ghosh2.5k
India
Arup Ghosh2.5k wrote:

There is no issue with the annotation, the Ensembl ids with missing Entrez annotation are unique to Ensembl. Check the attached article for an overview of all the annotation databases.

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1308-8

ADD COMMENTlink written 12 weeks ago by Arup Ghosh2.5k

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?

ADD REPLYlink written 11 weeks ago by mbk0asis530

No, I meant to say some genomic features only has an annotation only in Ensembl database , not in Entrez.

ADD REPLYlink written 11 weeks ago by Arup Ghosh2.5k
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