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
•
written
by
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.
•
written
by
Mehvi khan •
No problem, we wish you well, and please do come again if you need further assistance.
Log in to answer this question.
What is the output to
head(rownames(sorted_resultsA1))?^^^ this
When you search with the
geneIDyou need to be looking at the GENE database: https://www.ncbi.nlm.nih.gov/gene/?term=3005EntrezID for
CEACAM1gene is this: https://www.ncbi.nlm.nih.gov/gene/634Yes but why is OP getting CEACAM1 as result for a query that has 3005 as a key?
Not sure. Perhaps the ID's they have are not EntrezID but some other kind of ID?