I am attempting to run MAplot(), csScatter  and  plot functions using the cuff object created from readCufflinks tool in the cummeRbund package and I am getting the following error: 

Sometimes this error does not occur and I get a blank graph

The other plotting functions worked fine (dispersionPlot(),fpkmSCVPlot(),csBoxplot()

Here is the console:

csScatter(isoforms(cuff_egfp), "EGFP_DMSO", "EGFP_MG132", smooth=T)
Error in .local(object, x, y, logMode, pseudocount, labels, smooth, ...) : 
  One or more values of 'x' or 'y' are not valid sample names!

Here is the sessionInfo()
 

R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib