[BioC] question regarding using cummeRbund package

Hervé Pagès hpages at fhcrc.org
Mon Jul 2 21:35:31 CEST 2012 

On 07/02/2012 12:33 PM, Jack Luo wrote:
> 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
                  ^^^^^
              Here you go.

H.


> [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 at fhcrc.org> 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"
>>>> 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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>>>>>>
>>>>>          [[alternative HTML version deleted]]
>>>>>
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>>>>
>>>>
>>>
>>
>
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>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
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