Please look at the following code:

> library("org.Hs.eg.db")

> get("MAK", org.Hs.egALIAS2EG)
$MAK
[1] "4117"  "57538"

> get("ALPK3", org.Hs.egALIAS2EG)
$ALPK3
[1] "57538"

As far as I can tell, "MAK" is correctly mapped to the gene ID 4177 and incorrectly mapped to the gene id 57538 (the latter is the id corresponding to gene symbol "ALPK3").

Am I misunderstanding/misusing something?

Aris Floratos
Columbia University

You are confusing ALIAS and SYMBOL. The gene that currently has the HUGO symbol of ALPK3 has been known in the past as MAK. So if you ask for the ALIAS, you get all the genes that have ever been called MAK, and that includes the one that is currently called MAK, as well as ALPK3, which used to be called MAK.

If you just want the current SYMBOL, then you should ask for that. And you should also stop using get, and start using select.

> select(org.Hs.eg.db, c("MAK","ALPK3"), "ENTREZID","SYMBOL")
'select()' returned 1:1 mapping between keys and columns
  SYMBOL ENTREZID
1    MAK     4117
2  ALPK3    57538
> select(org.Hs.eg.db, c("MAK","ALPK3"), "ENTREZID","ALIAS")
'select()' returned 1:many mapping between keys and columns
  ALIAS ENTREZID
1   MAK     4117
2   MAK    57538
3 ALPK3    57538