[BioC] question regarding using cummeRbund package

[Valerie Obenchain]

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
>>>
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>>>
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>
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