Hi,

length(res$geneID)
[1] 45487

      allgenes = bitr(res$geneID, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Hs.eg.db",drop=FALSE)

'select()' returned 1:many mapping between keys and columns

Warning message:
In bitr(res$geneID, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = "org.Hs.eg.db",  :
  32.63% of input gene IDs are fail to map...

> length(allgenes$ENTREZID)
[1] 44399

I don´t understand why bitr does not return the same number of entries it has read as input. I would expect 45487 entries to be returned with NA for missing values. Am i missing something ?

> geneID = as.character(1:100)
> allgenes = bitr(geneID, toType="SYMBOL", fromType="ENTREZID", OrgDb="org.Hs.eg.db",drop=FALSE)
'select()' returned 1:1 mapping between keys and columns
Warning message:
In bitr(geneID, toType = "SYMBOL", fromType = "ENTREZID", OrgDb = "org.Hs.eg.db",  :
  17% of input gene IDs are fail to map...
> dim(allgenes)
[1] 100   2
> head(allgenes)
  ENTREZID SYMBOL
1        1   A1BG
2        2    A2M
3        3  A2MP1
4        4   <NA>
5        5   <NA>
6        6   <NA>
>

I can't reproduce your issue. 

pls follow the guide and make a reproducible example.

Ok got the problem.

I have duplicated geneIDS so the number of input ids is different from the returned number of entries. 

 geneID = c("1","2","3","3")
allgenes = bitr(geneID, toType="SYMBOL", fromType="ENTREZID", OrgDb="org.Hs.eg.db",drop=FALSE)
'select()' returned 1:1 mapping between keys and columns
 allgenes
  ENTREZID SYMBOL
1        1   A1BG
2        2    A2M
3        3  A2MP1

Ok thanks, i will match the ids back to my original table...