[BioC] question regarding using cummeRbund package

[Dan Tenenbaum]

Hi Jack,

On Fri, Jun 29, 2012 at 1:41 PM, Jack Luo <jluo.rhelp at 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
>
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>
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