cummerBund -> Doesn't see my samples

[madkitty]

I have 3 samples in 3 folders under the working directory of R, I did "Change directory" and pointed out one new folder "data" under the root C. "Data" contains our 3 samples outputed from cuffdiff.

• ~/Sample1
• ~/Sample2
• ~/Sample3

How can I point to R the directory for each sample in one readCufflinks command?
If I just call readCufflinks() it returns 0 sample ..

     > cuff<-readCufflinks()
     > cuff
     CuffSet instance with:
         0 samples
         0 genes
         0 isoforms
         0 TSS
         0 CDS
         0 promoters
         0 splicing
         0 relCDS

I need to execute the following, and retrieve cuff, dispersion graph, density graph and boxplot graph:

> cuff<-readCufflinks(system.file("extdata", package="cummeRbund"))
> cuff 

> disp<-dispersionPlot(genes(cuff))
> disp

> genes.scv<-fpkmSCVPlot(genes(cuff)) 
> isoforms.scv<-fpkmSCVPlot(isoforms(cuff))

> dens<-csDensity(genes(cuff)) 
> dens

> b<-csBoxplot(genes(cuff)) 
> b

[TiborNagy]

setwd('Sample1')
cuff1 <- readCufflinks()
setwd('../Sample2')
cuff2 <- readCufflinks()
setwd('../Sample3')
cuff3 <- readCufflinks()