Hi Kaspar, Ah, ok I had a look at the data contained with data() and it seems to be called golubTrain in my current package version. Funny is, I thought I would have the newest version if I installed the package with biocLite("golubEsets") just a few days ago !? Whatever, I can load it now and will make sure to update to the 1.4.2 version. Thanks for your help... Regards and a nice christmas time Benjamin -----Urspr?ngliche Nachricht----- Von: Kasper Daniel Hansen [mailto:khansen at stat.Berkeley.EDU] Gesendet: 21 December 2006 14:41 An: Benjamin Otto Cc: 'Seth Falcon'; bioconductor at stat.math.ethz.ch Betreff: Re: [BioC] Where do I find the golub_Train dataset? You are way behind regarding your version of golubEsets. I just installed it from BioC 1.9 using getBioC, and my version is 1.4.2. So update :) However, in that version, it is called R> data(Golub_Train) however, that may be a new term. You can always see what datasets you have available you typing R> data() (this is of course for packages attached by a library command), so R> library(golubEsets) R> data() gives me (I have deleted output from other packages such as datasets) <r output=""> Data sets in package 'golubEsets': Golub_Merge Combined Test and Training Sets from the Golub Paper Golub_Test Test Set Data from the Golub Paper Golub_Train Training Set from the Golub Paper golubMerge Combined Test and Training Sets from the Golub Paper golubTest Test Set Data from the Golub Paper golubTrain Training Set from the Golub Paper Use 'data(package = .packages(all.available = TRUE))' to list the data sets in all *available* packages. <end r="" output=""> That should give you enough to get your problem solved. Kasper On Dec 21, 2006, at 2:14 PM, Benjamin Otto wrote: > Hi Seth, Hi Kyle, > > I admitt I have written "golub_Train" in my mail. However that is NOT > the problem! I used "Golub_Train" and certain other upper/lower case > combinations before submitting to the bioclist without success. > Besides, I > tried to make a copy and paste of the example and the problem persists > so it's not a typo. I do have the golubEsets package installed, I even > made sure to have the newest version installed which is, according to > my knowledge, version 1.0.1. > > Here is my session info: > > R version 2.4.0 (2006-10-03) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] "tools" "grid" "methods" "stats" "graphics" > "grDevices" > [7] "utils" "datasets" "base" > > other attached packages: > Biobase golubEsets hu6800 quantsmooth quantreg > SparseM > "1.12.2" "1.0.1" "1.10.0" "1.0.0" "4.03" > "0.71" > lodplot gplots gdata gtools > "1.0" "2.3.1" "2.1.1" "2.1.1" > > And THIS is the message I receive when submitting the command > >> data(Golub_Train) > Warning message: > data set 'Golub_Train' not found in: data(Golub_Train) > > > Any further suggestions? Thanks for your help. :-) > > Regards, > > Benjamin > > > > -----Urspr?ngliche Nachricht----- > Von: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag von Seth > Falcon > Gesendet: 19 December 2006 16:49 > An: bioconductor at stat.math.ethz.ch > Betreff: Re: [BioC] Where do I find the golub_Train dataset? > > "Benjamin Otto" <b.otto at="" uke.uni-hamburg.de=""> writes: > >> Dear list members, >> >> Where do I find the "golub_Train" dataset. It is used in the idiogram >> package example however I neither can find it anywhere in the bioc >> package or CRAN repositories nor does it seem to be part of the >> golubEsets package. > > If you read the example carefully, you will find: > > if(require(hu6800) && require(golubEsets)) { > library(golubEsets) > data(Golub_Train) > > In any case, you want to install the golubEsets package. You can do > so using biocLite. > > + seth > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor