Hello everyone, 

I used different tools to convert human gene ensemble ID to ENTREZ but each of them seems to have problems like:
-BioMart does not recognizes all the ensemble ID but barely 30% , 
-BioDBnet ...I couldn't make it working cause I could only select the type of output ,
-DAVID gives me lots of false duplicates.

What do you usually use for this work ? 

thank you 


You can use `AnnotationDbi` to convert Ensembl ids. The code snippet converts Ensembl id to Entrez ids.

    library("AnnotationDbi")
    library("org.Hs.eg.db")
    #columns(org.Hs.eg.db) # returns list of available keytypes
    data$entrez = mapIds(org.Hs.eg.db,
                        keys=row.names(data), #Column containing Ensembl gene ids
                        column="ENTREZID",
                        keytype="ENSEMBL",
                        multiVals="first")