Error for converting from gene symbol to Entrez IDs
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modarzi ▴ 10
@modarzi-16296
Last seen 3.4 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 • 1.0k views
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@james-w-macdonald-5106
Last seen 45 minutes 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.

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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.

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