[BioC] question regarding using cummeRbund package

[Dan Tenenbaum]

Hi Jack,

On Mon, Jul 2, 2012 at 12:01 PM, Jack Luo <jluo.rhelp at 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 at 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 at fhcrc.org>
>>> wrote:
>>>
>>>> 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
>>>>>
>>>>>         [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at 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 at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>