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 Warning messages: 1: In find.package(package, lib.loc, verbose = verbose) :   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]]

On Fri, Jan 25, 2013 at 2:55 PM, carol white <wht_crl at="" yahoo.com=""> 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: Hi, Carol. You need to load the library first. library(colonCA) Then, you should be good-to-go. Sean > In data(colonCA) : data set ?colonCA? not found > > When I load with (data colonCA, lib.loc = "path to colonCA"), I get the messages > > > Warning messages: > 1: In find.package(package, lib.loc, verbose = verbose) : > 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

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) : > ? 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