Received a suggestion from Jim MacDonald to look for and extract this zip file, and then try to load. C:\Program Files\R\rw2001\library\yeastCC\data\Rdata.zip Extracted this zip file which created yeastCC.RData, which is a file of type "R Workspace". Then dragged yeastCC.Rdata onto the RGui to do the load as shown here: > load("C:/Program Files/R/rw2001/library/yeastCC/data/Rdata/yeastCC.RData") Although still get same error: > library(yeastCC) Error in open.connection(con, "rb") : unable to open connection In addition: Warning message: cannot open compressed file `C:/PROGRA~1/R/rw2001/library/yeastCC/data/yeastCC.RData' Error in library(yeastCC) : .First.lib failed for 'yeastCC' > and don't see yeastCC in packages: > (.packages()) [1] "multtest" "genefilter" "survival" "splines" "affy" "reposTools" "annotate" [8] "Biobase" "tools" "methods" "stats" "graphics" "grDevices" "utils" [15] "datasets" "base" > and get warning with data command: > data(yeastCC) Warning message: Data set 'yeastCC' not found in: data(yeastCC) > exprs works: > dat <- exprs(yeastCC) > dim(dat) [1] 6178 77 > and see data: > dat[1:5,1:5] cln3.1 cln3.2 clb2.2 clb2.1 alpha0 YAL001C 0.15 NA -0.22 0.07 -0.15 YAL002W -0.07 -0.76 -0.12 -0.25 -0.11 YAL003W -1.22 -0.27 -0.10 0.23 -0.14 YAL004W -0.09 1.20 0.16 -0.14 -0.02 YAL005C -0.60 1.01 0.24 0.65 -0.05 > Thanks, John Garner

On Feb 5, 2005, at 10:04 PM, JDCGo@aol.com wrote: > Received a suggestion from Jim MacDonald to look for and extract this > zip file, and then try to load. > > C:\Program Files\R\rw2001\library\yeastCC\data\Rdata.zip > > Extracted this zip file which created yeastCC.RData, which is a file > of type "R Workspace". Then dragged yeastCC.Rdata onto the RGui to do > the load as shown here: > I'm pretty confused by what you are doing. In R, if you want to access data from a package, like yeastCC, you first install the package. All that that does is to download it and put it in the right place. You need to use R's tools for doing that: on windows either use the menu or install.packages("yeastCC"). You cannot download the zip file and unpack it, since R does some manipulation on the files when it installs them. So if you have not installed this way, then you should do it this way. Then, any (and hence every) time you want to use the package you will need to load it. so library("yeastCC") does that. Then search(), should report that it is there (I have no concept of why you are calling .packages() ) At this point data(), with no arguments will list all the data sets you have access to. Data in packages that are installed, but not loaded (or attached) is not available. Data in packages that were incorrectly installed (using unzip, for example) are also not available. Why are you calling load? It would help if you could point me to the documentation that gave you some of these ideas, as I would like to try and correct it. There is rather a lot (like the Introduction to R) that should give you somewhat better instructions. Robert >> load("C:/Program >> Files/R/rw2001/library/yeastCC/data/Rdata/yeastCC.RData") > This will load exactly the data file, but it is certainly not the recommended way to do that. If it worked without error then you do have a data file at the location given by that path. > Although still get same error: > >> library(yeastCC) > Error in open.connection(con, "rb") : unable to open connection So your library was not correctly installed, not much good can happen until this is fixed. > In addition: Warning message: > cannot open compressed file > `C:/PROGRA~1/R/rw2001/library/yeastCC/data/yeastCC.RData' > Error in library(yeastCC) : .First.lib failed for 'yeastCC' Yes, well a comparison of this path with the one above certainly ought to suggest what the problem is. >> > > and don't see yeastCC in packages: > >> (.packages()) > [1] "multtest" "genefilter" "survival" "splines" "affy" > "reposTools" "annotate" > [8] "Biobase" "tools" "methods" "stats" "graphics" > "grDevices" "utils" > [15] "datasets" "base" >> > Well, you got an error loading, why do you suppose it would have loaded anyways? And as I said above use search(), to see which packages are attached. > and get warning with data command: > >> data(yeastCC) > Warning message: > Data set 'yeastCC' not found in: data(yeastCC) >> Yes, well, again, you got that error message above, repeating the command, will give you the same error message. > > exprs works: > >> dat <- exprs(yeastCC) >> dim(dat) > [1] 6178 77 >> > And again, you directly loaded the data, using load, so it is there, no surprise, your sequence of commands, and the errors and warnings seem to suggest that the package is incorrectly installed. I would try to fix that first. Robert > and see data: > >> dat[1:5,1:5] > cln3.1 cln3.2 clb2.2 clb2.1 alpha0 > YAL001C 0.15 NA -0.22 0.07 -0.15 > YAL002W -0.07 -0.76 -0.12 -0.25 -0.11 > YAL003W -1.22 -0.27 -0.10 0.23 -0.14 > YAL004W -0.09 1.20 0.16 -0.14 -0.02 > YAL005C -0.60 1.01 0.24 0.65 -0.05 >> > > Thanks, > > John Garner > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+

That's not what I suggested. After you unzip that file (leaving it in the data directory), you should then access the package in the usual way, which is to do: library(yeastCC) Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> <jdcgo@aol.com> 02/06/05 1:04 AM >>> Received a suggestion from Jim MacDonald to look for and extract this zip file, and then try to load. C:\Program Files\R\rw2001\library\yeastCC\data\Rdata.zip Extracted this zip file which created yeastCC.RData, which is a file of type "R Workspace". Then dragged yeastCC.Rdata onto the RGui to do the load as shown here: > load("C:/Program Files/R/rw2001/library/yeastCC/data/Rdata/yeastCC.RData") Although still get same error: > library(yeastCC) Error in open.connection(con, "rb") : unable to open connection In addition: Warning message: cannot open compressed file `C:/PROGRA~1/R/rw2001/library/yeastCC/data/yeastCC.RData' Error in library(yeastCC) : .First.lib failed for 'yeastCC' > and don't see yeastCC in packages: > (.packages()) [1] "multtest" "genefilter" "survival" "splines" "affy" "reposTools" "annotate" [8] "Biobase" "tools" "methods" "stats" "graphics" "grDevices" "utils" [15] "datasets" "base" > and get warning with data command: > data(yeastCC) Warning message: Data set 'yeastCC' not found in: data(yeastCC) > exprs works: > dat <- exprs(yeastCC) > dim(dat) [1] 6178 77 > and see data: > dat[1:5,1:5] cln3.1 cln3.2 clb2.2 clb2.1 alpha0 YAL001C 0.15 NA -0.22 0.07 -0.15 YAL002W -0.07 -0.76 -0.12 -0.25 -0.11 YAL003W -1.22 -0.27 -0.10 0.23 -0.14 YAL004W -0.09 1.20 0.16 -0.14 -0.02 YAL005C -0.60 1.01 0.24 0.65 -0.05 > Thanks, John Garner _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.