converting Gene ID to GeneSymbols

Question

[Mehvi khan]

Hello

I am converting the geneids into Gene symbol using the map function. The conversion is going fine without any error but when I am checking online on ncbi website its showing a different symbol for that geneid . the following is the code that I am using

sorted_resultsA1$Symbol <- mapIds(org.Hs.eg.db, keys = row.names(sorted_resultsA1),column ="SYMBOL",keytype = "ENTREZID")

and the output for this is :

             GeneId            Symbol
GeneID:3005        CEACAM1
GeneID:1308        APOBEC1
GeneID:100506013     TLE5

where as when I searched for these ids in the ncbi gene page I got the following result

3005    < -       Official Symbol                              Official Full Name
1308              H1-0  provided by HGNC                   H1.0 linker histoneprovided by HGNC
100506013     Official Symbol                         Official Full Name
                    APELA provided by HGNC                             apelin receptor early endogenous ligand

Kindly guide and suggest any solution.

Thank you

[Ram]

What is the output to head(rownames(sorted_resultsA1))?

[Kevin Blighe]

^^^ this

[GenoMax]

When you search with the geneID you need to be looking at the GENE database: https://www.ncbi.nlm.nih.gov/gene/?term=3005

EntrezID for CEACAM1 gene is this: https://www.ncbi.nlm.nih.gov/gene/634

[Ram]

Yes but why is OP getting CEACAM1 as result for a query that has 3005 as a key?

[GenoMax]

Not sure. Perhaps the ID's they have are not EntrezID but some other kind of ID?

Answer 1

[Mehvi khan]

Thank you so much, issue resolved .

Yes the row is a name of a column in the sorted_resultsA1 which has the gene ids, and I was mistakenly taking the row names.

Thanks again, really appreciate your help.

[Kevin Blighe]

No problem, we wish you well, and please do come again if you need further assistance.

[Ram]

Please accept your answer to mark the post as solved.