Question: Error for converting from gene symbol to Entrez IDs
0
gravatar for modarzi
6 months ago by
modarzi70
modarzi70 wrote:

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,

ADD COMMENTlink modified 6 months ago • written 6 months ago by modarzi70
1

The error is clear, they are not valid symbol names. Are you sure these are valid gene symbols for zebrafish??

ADD REPLYlink written 6 months ago by Benn6.6k

Hi,

Thanks for your comment. No, my genes symbols belongs for Human. based on your comment If I can't use this package for Human genes symbols, what should I do? which package can give me Entrez IDs from my symbols? I appreciate if you share his/her comment with me. Best Regards,

ADD REPLYlink modified 6 months ago • written 6 months ago by modarzi70

If you want homology between human and Danio genes, try biomaRt. There is an example in 4.11 how to use both human and mouse databases, try to see if you can do it yourself for human/Danio.

https://www.bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html

ADD REPLYlink written 6 months ago by Benn6.6k
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