I am working with Arabidopsis. For the last one week I have had a good time with cummeRbund.. but I want R to give me the results in real-time.. by this I mean.. I need the gene names..  I found the following R-script. CAN SOMEone help me modify this for my need..  I am using Arabidopsis and have pulled out the cuffdiff output into a folder on desktop. I managed to set up my working directory one level up in my documents.
My samples are not replicated.. I know it is a problem but with 3 mutants one wild type and two conditions.. (a total of 8 samples), I could not afford replicating my samples in Illumina.. It would have cost me a fortune.. so I replicated the samples and pooled their RNA before submission for RNAsequencing. 
Have a great weekend wherever you are.

library(cummeRbund)
myDir <- system.file("extdata", package="cummeRbund") 
gtfFile <- system.file("extdata/chr1_snippet.gtf",package="cummeRbund")

cuff <- readCufflinks(dir=myDir,gtfFile=gtfFile,genome="hg19",rebuild=TRUE)