Hi, a quick check on NCBI Gene reveals that the official symbol for this is *PRXL2C*, not *AAED1*. In this way, I would not have expected `org.Hs.eg.db` (using ‘recent’ annotation) to have it. However, I can see that `EnsDb.Hsapiens.v86` (older version) does [have it]. So, there must have been an annotation change in the recent Ensembl versions. Important to remember that gene annotation is constantly changing.
# org.Hs.eg.db
library(org.Hs.eg.db)
select(org.Hs.eg.db,
keys=”AAED1″,
column = c(‘ENSEMBL’, ‘SYMBOL’),
keytype=”SYMBOL”)
Error in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are valid keys for ‘SYMBOL’. Please use the keys method to see a listing of valid arguments.
# EnsDb.Hsapiens.v86
library(EnsDb.Hsapiens.v86)
select(EnsDb.Hsapiens.v86,
keys=”AAED1″,
column = c(‘GENEID’, ‘SYMBOL’),
keytype=”SYMBOL”)
GENEID SYMBOL
1 ENSG00000158122 AAED1
# ————
If we instead check for the official symbol, *PRXL2C*, in `org.Hs.eg.db`:
select(org.Hs.eg.db,
keys=”PRXL2C”,
column = c(‘ENSEMBL’, ‘SYMBOL’),
keytype=”SYMBOL”)
SYMBOL ENSEMBL
1 PRXL2C ENSG00000158122
# ———-
In situations like this, one can use *limma*’s `alias2SymbolTable()` to help retrieve all aliases for your genes.
limma::alias2SymbolTable(‘AAED1′, species=”Hs”)
[1] “PRXL2C”
This simple example also highlights why it’ …