[BioC] DESeq gene names under id

[Mary Ann Allen]

R novice here, trying to use DESeq (which is working well, by the way)

In the manual "Analysing RNA-Seq data with the\DESeq" package" I 
followed the directions exactly. However, I get something slightly 
different. 
http://bioconductor.org/packages/2.9/bioc/vignettes/DESeq/inst/doc/DESeq.pdf

When I use the command (page 7)
res <- nbinomTest( cds, "N", "T" )

I get numbers under ids because on page 4 we removed the gene names.
countsTable <- countsTable[ , -1 ]

How can i get my res to match what is in the manual with gene names 
under id?

Thanks,
Mary Ann Allen