[BioC] bioc data set not found

[James W. MacDonald]

Hi Carol,

On 1/25/2013 2:55 PM, carol white wrote:
> Hi,
> It might be a simple question but how is it possible to load a bioc data set like colonCA? As a user, I installed Biobase, BiocInstaller and colonCA in my environment. Then, when I load Biobase (library Biobase) and colonCA (data colonCA), I get the following message
>
> Warning message:
> In data(colonCA) : data set ‘colonCA’ not found
>
> When I load with (data colonCA, lib.loc = "path to colonCA"), I get the messages

You have to load the colonCA package first, just like any other R 
package. So something like

library(colonCA)
data(colonCA)

should get you where you want to go. Some packages have more than one 
data set in them, and you can get a listing by

data(package = "colonCA")

It so happens that this package only has the colonCA dataset.

Best,

Jim


>
>
> Warning messages:
> 1: In find.package(package, lib.loc, verbose = verbose) :
> Â  there is no package called
>   ‘stats’
> 2: In find.package(package, lib.loc, verbose = verbose) :
>   there is no package called ‘graphics’
> 3: In find.package(package, lib.loc, verbose = verbose) :
>   there is no package called ‘grDevices’
> 4: In find.package(package, lib.loc, verbose = verbose) :
>   there is no package called ‘utils’
> 5: In find.package(package, lib.loc, verbose = verbose) :
>   there is no package called ‘datasets’
> 6: In find.package(package, lib.loc, verbose = verbose) :
>   there is no package called ‘methods’
> 7: In find.package(package, lib.loc, verbose = verbose) :
>   there is no package called ‘base’
> 8: In data(colonCA, lib.loc = "path to colonCA") :
>   data set ‘colonCA’ not found
> which searches the packages that are in
>
> /usr/lib/R/library/
>
> Alternatively, I installed colonCA in /usr/lib/R/library/ as root but got the same msg
>
> data set ‘colonCA’ not found
>
> Look forward to your solution
>
> Carol
>
> 	[[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

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099