Where do I find the golub_Train dataset?
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Benjamin Otto ▴ 830
@benjamin-otto-1519
Last seen 8.2 years ago
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. Best regards, Benjamin Otto -- Benjamin Otto Universitaetsklinikum Eppendorf Hamburg Institut fuer Klinische Chemie Martinistrasse 52 20246 Hamburg
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 8.2 years ago
"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
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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
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To add to the last post -- If memory serves, there was a name change between golubEsets 1.0.1 and the more recent versions (1.2.4) The current "Golub_Train" dataset (1.2.4) was named "golubTrain" in 1.0.1 package I think the example will work if either a) get golubEsets 1.2.4 or b) use the old name of "golubTrain" -kyle > From: Benjamin Otto <b.otto at="" uke.uni-hamburg.de=""> > Date: Thu, 21 Dec 2006 14:14:46 +0100 > To: 'Seth Falcon' <sfalcon at="" fhcrc.org="">, <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] Where do I find the golub_Train dataset? > > 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 This email message, including any attachments, is for the so...{{dropped}}
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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
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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
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Furge, Kyle ▴ 210
@furge-kyle-501
Last seen 8.2 years ago
R is case-sensitive. Instead of "golub_Train" try "Golub_Train". -kyle > From: Benjamin Otto <b.otto at="" uke.uni-hamburg.de=""> > Date: Tue, 19 Dec 2006 15:30:41 +0100 > To: <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] Where do I find the golub_Train dataset? > > 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. > > Best regards, > > Benjamin Otto > > -- > Benjamin Otto > Universitaetsklinikum Eppendorf Hamburg > Institut fuer Klinische Chemie > Martinistrasse 52 > 20246 Hamburg > > _______________________________________________ > 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 This email message, including any attachments, is for the so...{{dropped}}
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 8.2 years ago
"Benjamin Otto" <b.otto at="" uke.uni-hamburg.de=""> writes: > 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 !? Are you sure that's what you did? I would be very surprised to learn that biocLite installed a stale version for you. If so, please send us details. + seth
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