Hey, there,

I was following the instruction of http://www.bioconductor.org/help/workflows/rnaseqGene/#annotate to update the annotation in my DEG files.  I used the code they designed: 

convertIDs <- function( ids, from, to, db, ifMultiple=c("putNA", "useFirst")) {
  stopifnot( inherits( db, "AnnotationDb" ) )
  ifMultiple <- match.arg( ifMultiple )
  suppressWarnings( selRes <- AnnotationDbi::select(
    db, keys=ids, keytype=from, columns=c(from,to) ) )
  if ( ifMultiple == "putNA" ) {
    duplicatedIds <- selRes[ duplicated( selRes[,1] ), 1 ]
    selRes <- selRes[ ! selRes[,1] %in% duplicatedIds, ]
  }
  return( selRes[ match( ids, selRes[,1] ), 2 ] )
}

I loaded my DEG csv file to deg_01 first. The id column has all the refseq ids.

Then

> deg_01$newMGI_symbol <- convertIDs("deg_01$id", "REFSEQ", "SYMBOL", org.Mm.eg.db)

 Error in .testForValidKeys(x, keys, keytype) : 
  None of the keys entered are valid keys for 'REFSEQ'. Please use the keys method to see a listing of valid arguments. 

I checked and the deg_01$id are all refseq ids.

> deg_01$id
  [1] NM_026268    NM_025777    NM_013478    NR_015524    NM_001099297 NM_177610    NM_001122954
  [8] NM_144834    NM_011110    NM_016668    NM_013820    NM_001145874 NM_001081060 NM_080457   
 [15] NM_007646    NM_020279    NM_172415    NM_007686    NM_001112723 NM_001173505 NM_001290565
 

Any suggestions? Thanks.

Great. Thanks for your help. 

I followed your suggestion and did:

> deg_01$newMGI_symbol <- convertIDs(as.character(deg_01$id), "REFSEQ", "SYMBOL", org.Mm.eg.db)

It worked. I did not know that factor vs character makes such a difference because the same input works well with biomaRt .