Sure, see below:

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] cummeRbund_1.2.0    reshape2_1.2.1      ggplot2_0.9.1
[4] RSQLite_0.11.1      DBI_0.2-5           BiocInstaller_1.4.7

loaded via a namespace (and not attached):
 [1] colorspace_1.1-1   dichromat_1.2-4    digest_0.5.2       grid_2.15.1

 [5] labeling_0.1       MASS_7.3-19        memoise_0.1        munsell_0.3

 [9] plyr_1.7.1         proto_0.3-9.2      RColorBrewer_1.0-5 scales_0.2.1

[13] stringr_0.6        tools_2.15.1

Thanks,

-Jack

On Mon, Jul 2, 2012 at 3:06 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

> Hi Jack,
>
> On Mon, Jul 2, 2012 at 12:01 PM, Jack Luo <jluo.rhelp@gmail.com> wrote:
> > Hi Val,
> >
> > Thanks. See below:
> >
> >> library(cummeRbund)
> >> cuff <- readCufflinks(dir=system.file("extdata", package="cummeRbund"))
> >> disp<-dispersionPlot(genes(cuff))
> > Error: could not find function "dispersionPlot"
> >> dens<-csDensity(genes(cuff))
> >> densRep<-csDensity(genes(cuff),replicates=T)
> >> b<-csBoxplot(genes(cuff))
> >> b
> >> brep<-csBoxplot(genes(cuff),replicates=T)
> >> brep
> >> s<-csScatter(genes(cuff),"hESC","Fibroblasts",smooth=T)
> >> s
> >> dend<-csDendro(genes(cuff))
> >> dend.rep<-csDendro(genes(cuff),replicates=T)
> > Error in csDendro(genes(cuff), replicates = T) :
> >   unused argument(s) (replicates = T)
> >>
> >> m<-MAplot(genes(cuff),"hESC","Fibroblasts")
> >> m
> > Warning message:
> > Removed 57 rows containing missing values (geom_point).
> >> mCount<-MAplot(genes(cuff),"hESC","Fibroblasts",useCount=T)
> > Error in .local(object, x, y, logMode, pseudocount, ...) :
> >   unused argument(s) (useCount = TRUE)
> >> mCount
> > Error: object 'mCount' not found
> >
>
> That is helpful but we still need the output of
>
> sessionInfo()
>
> because that tells us what platform you're on, what version of R you
> are running, and what version of various packages you have loaded.
> Run the sessionInfo command after loading cummeRbund.
>
> Thanks,
> Dan
>
>
> >
> > Let me know if that's what you need, thanks.
> >
> > -Jack
> >
> > On Sun, Jul 1, 2012 at 5:52 PM, Valerie Obenchain <vobencha@fhcrc.org>
> > wrote:
> >>
> >> Jack,
> >>
> >> In order for us to help we need some more information.
> >>
> >> Please provide a small reproducible example of the code you are
> executing
> >> and the error. Below you've provided the errors but no preceding code.
> Also
> >> send the output of typing sessionInfo() at the command prompt.
> >>
> >> fyi, I've cc'd the package maintainer.
> >>
> >> Valerie
> >>
> >>
> >>
> >>
> >> On 07/01/12 05:50, Jack Luo wrote:
> >>>
> >>> 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]]
> >>>
> >>> _______________________________________________
> >>> 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
> >>
> >>
> >
>

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