Hi Dan,

Thanks for your email. Yeah, I installed the package using
biocLite("cummeRbund"). There are some functions that work well, but not
those functions I listed for error msg, not sure why.

Thanks,

-Jack

On Fri, Jun 29, 2012 at 4:56 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

> Hi Jack,
>
> On Fri, Jun 29, 2012 at 1:41 PM, Jack Luo <jluo.rhelp@gmail.com> wrote:
> > 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.
>
> Although the vignette says you need cufflinks, you don't, really. You
> just need some files produced by cufflinks.
>
> >
> > 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)
> >
>
> How did you install cummeRbund?
> Try installing it as follows:
> biocLite("cummeRbund")
>
> Also, when reporting errors, please report the command(s) that caused
> the errors and include the output of sessionInfo().
>
> Thanks,
> Dan
>
>
> > There are some other similar errors.
> >
> > Thanks,
> >
> > -Jack
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

