[BioC] question regarding using cummeRbund package

[Hervé Pagès]

Hi Jack,

On 07/02/2012 12:06 PM, Dan Tenenbaum wrote:
> 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"

It looks like the dispersionPlot() function is new in cummeRbund
version 1.99.* (BioC devel), so your problem is very likely that
you're trying to run code that belongs to the vignette of cummeRbund
1.99.* while you have some older version of the package installed.
Hard to know for sure without you providing the output of your
sessionInfo(). In any case, make sure you look at the right
vignette/examples i.e. that they belong to the package you are
actually using. For example using browseVignettes() is a much
safer way than picking the vignette from somewhere on the web e.g.
from http://bioconductor.org/packages/2.11/bioc/html/cummeRbund.html
This is because browseVignettes() shows you the list of vignettes
that belong to the packages you installed so they are guaranteed to
match.

Cheers,
H.


>>> 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]]
>>>>>>
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>>>>>
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>          [[alternative HTML version deleted]]
>>>>
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>>>
>>>
>>
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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