The conversion of probe ids to entrez ids is quite straight forward

   i1<-c("246653_at", "246897_at", "251347_at", "252988_at", "255528_at", "256535_at", "257203_at", "257582_at", "258807_at", "261509_at", "265050_at", "265672_at")

 select(ath1121501.db, i1, "ENTREZID", "PROBEID")

     PROBEID ENTREZID
 1  246653_at   833474
 2  246897_at   832631
 3  251347_at   825272
 4  252988_at   829998
 5  255528_at   827380
 6  256535_at   840223
 7  257203_at   821955
 8  257582_at   841494
 9  258807_at   819558
 10 261509_at   843504
 11 265050_at   841636
 12 265672_at   817757

But Iam unsure how to do it for a long list of lists resulting from a clustering and store it as a list of ENTREZ ids instead of probe ids again:

For instance:

    List 
             [[1]]
     247964_at   248684_at   249126_at   249214_at   250223_at   253620_at   254907_at                 259897_at   261256_at 267126_s_at 
     28          40          44          45          54          95         108         152         171         229 
             [[2]]
    248230_at 250869_at 259765_at 265948_at 266221_at 
    33        64       151       216       221 
             [[3]]
        245385_at   247282_at   248967_at   250180_at   250881_at   251073_at  53874_at     256093_at   257054_at   260007_at 
      5          22          42          52          65          67         101           117         125         155 
      261868_s_at   263136_at   267497_at 
       181         195         232

It should be something like

   [[1]]
       "835761","834904","834356","834281","831256","829175","826721","843479","837084","816891",
   "816892"

and similarly for other list of lists. emphasized text