Question: Some symbols share the same ensembl ID in org.Hs.eg.db but not in ensembl website, how to deal with it?
0
gravatar for Timze W
12 months ago by
Timze W20
Timze W20 wrote:

Hello, as a newbie, I do get some troubles in converting ensembl ID to gene SYMBOL.

For example, when I convert the "ENSG00000158164" to SYMBOL in the R library "org.Hs.eg.db", it has 2 symbol names. This is my code and output:

> select(org.Hs.eg.db, keys="ENSG00000158164",columns=c("CHR","SYMBOL","GENENAME"), keytype="ENSEMBL")
'select()' returned 1:many mapping between keys and columns
          ENSEMBL         CHR       SYMBOL          GENENAME
1 ENSG00000158164    X        TMSB15A         thymosin beta 15a
2 ENSG00000158164    X        TMSB15B         thymosin beta 15B

But actually the ensembl ID of TMSB15B is ENSG00000158427;

> select(org.Hs.eg.db, keys="ENSG00000158427",columns=c("CHR","SYMBOL","GENENAME"), keytype="ENSEMBL")
'select()' returned 1:1 mapping between keys and columns
          ENSEMBL.         CHR       SYMBOL          GENENAME
1 ENSG00000158427      X        TMSB15B       thymosin beta 15B

Could someone suggest me how to deal with it?

ADD COMMENTlink written 12 months ago by Timze W20
1

This looks like the results of a bug in the script that was used to make org.Hs.eg.db, can you report it to the package maintainer?

ADD REPLYlink modified 12 months ago • written 12 months ago by Devon Ryan88k
1

I will update this post as soon as there is new progress.

ADD REPLYlink written 12 months ago by Timze W20
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