Error in testForValidKeytype(x, keytype) : Invalid keytype: TAIR. Please use the keytypes method to see a listing of valid arguments.
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1627166123 • 0
@904bbf0b
Last seen 11 days ago
Taiwan

I used org.m.eg. db to do GO enrichment analysis, and the following error always appeared. I used the method in keytypes (org.m.eg. db), but it still could not be solved.

org.Mm.eg.db • 95 views
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1627166123 • 0
@904bbf0b
Last seen 11 days ago
Taiwan

res3$symbol <- mapIds(org.Mm.eg.db,

  • keys=res3$gene_id,
  • column="SYMBOL",
  • keytype="TAIR",
  • multiVals="first") Error in testForValidKeytype(x, keytype) : Invalid keytype: TAIR. Please use the keytypes method to see a listing of valid arguments.enter image description here
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Guido Hooiveld ★ 2.9k
@guido-hooiveld-2020
Last seen 14 hours ago
Wageningen University, Wageningen, the …

The keytype argument basically describes the type of identifier you would like to query on; for example is it an ENTREZID, or REFSEQ, or SYMBOL. You can check these by:

keytypes(org.Mm.eg.db)
 [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS"
 [6] "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL"  "GENENAME"    
[11] "GO"           "GOALL"        "IPI"          "MGI"          "ONTOLOGY"    
[16] "ONTOLOGYALL"  "PATH"         "PFAM"         "PMID"         "PROSITE"     
[21] "REFSEQ"       "SYMBOL"       "UNIGENE"      "UNIPROT"     

You defined keytype="TAIR". Please note that TAIR are Arabidopsis (plant) IDs! TAIR = The Arabidopsis Information Resource. Obviously, TAIR IDs are not in a mouse annotation library, hence the error you got! Invalid keytype: TAIR.

So your query should rather be:

res3$symbol <- mapIds(org.Mm.eg.db,
    keys=res3$gene_id,
    keytype="ENSEMBL",  #gene_id are ENSEMBL IDs!
    column=c("SYMBOL"), #the annotation info you would like to retrieve
    multiVals="first")

Be sure to also check the help pages of the function mapIds:

?mapIds

Lastly, since your primary IDs are ENSEMBL ids; why don't you use an EnsDB (instead of a NCBI-based OrgDb) for annotating? This thread may be useful to get started with an EnsDb.

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