gistfile1.r

library(cummeRbund)
packagePath <- system.file(package="cummeRbund")
extdataPath <- paste(packagePath, "/extdata", sep = "")
cuff <- readCufflinks(extdataPath,rebuild=TRUE)

my.fpkmMatrix <- fpkmMatrix(genes(cuff))

plot(x=my.fpkmMatrix$"hESC",
     y=my.fpkmMatrix$"Fibroblasts",
     log="xy",
     xlim=c(0.1,1E+06),ylim=c(0.1,1E+06),pch=20)

my.gene<- my.fpkmMatrix[which.max(my.fpkmMatrix$"hESC"),]

points(x=my.gene$"hESC",y=my.gene$"Fibroblasts",col="red",pch=19)