Question

Error for converting from gene symbol to Entrez IDs

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modarzi ▴ 10

@modarzi-16296

Last seen 4.2 years ago

Hi,

For my study, I have to convert gene symbols to Entrez IDs. So, by using "org.Dr.eg.db" package and my annotation file(annot) I wrote below code:

library("org.Dr.eg.db")

keytypes(org.Dr.eg.db)

k= c("RP11-34P13.7","DDX11L1","RP4-591L5.1" )
kname<- bitr(k, fromType="SYMBOL", toType=("ENTREZID"), OrgDb="org.Dr.eg.db")

unfortunately, I got this error:

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.

I appreciate if any body share his/her comment with me.

Best Regards,

org.Dr.eg.db Entrez ID • 1.3k views

ADD COMMENT • link updated 6.2 years ago by James W. MacDonald 67k • written 6.2 years ago by modarzi ▴ 10

score 2 · Answer 1 · 2018-10-21

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 3 days ago

United States

The gene symbols you are using are human, but you are trying to use the drosophila OrgDb. That won't work. You will either need to use the human OrgDb, or drosophila gene symbols. Or if you are trying to do orthology mapping, you could use getLDS from the biomaRt package.

ADD COMMENT • link 6.2 years ago James W. MacDonald 67k

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Correction: org.Dr.eg.db is for Zebrafish (Danio rerio). Use org.Hs.eg.db for Human (Homo sapiens), org.Dm.eg.db for Fruit Fly (Drosophila melanogaster). Annotation package names depend on the latin names for species.

ADD REPLY • link 5.9 years ago tom.kelly ▴ 10