For small tests, pre- and post-processing with Bioconductor, you can start an interactive R session on the login nodes. All other Bioconductor jobs have to be submitted through the batch system. You can submit a Bioconductor job (inputfile.R) in batch mode with the following command:
bsub [LSF options] "R --vanilla --slave < inputfile.R > outputfile"
Here you need to replace [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the wiki page about the batch system. In this case, stdout is redirected into "outputfile".