Hi,

I am a newbie to RNA-seq data and try to learn using the cummeRbund
package. Some simple questions are:

1. My OS is windows 7. I have no problem installing the cummeRbund in R,
but do I need to install cufflinks? I thought there is only linux and mac
version of cufflinks, not windows.

2. When I was running the example provided in:
http://bioconductor.org/packages/devel/bioc/vignettes/cummeRbund/inst/doc/cummeRbund-manual.pdf

I run into several errors:
A. Error: could not find function "dispersionPlot"
B. dend.rep<-csDendro(genes(cuff),replicates=T)
Error in csDendro(genes(cuff), replicates = T) :
  unused argument(s) (replicates = T)
C. mCount<-MAplot(genes(cuff),"hESC","Fibroblasts",useCount=T)
Error in .local(object, x, y, logMode, pseudocount, ...) :
  unused argument(s) (useCount = TRUE)

There are some other similar errors.

Thanks,

-Jack

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