[BioC] Where do I find the golub_Train dataset?

[Benjamin Otto]

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




-----Ursprüngliche 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
>
>
>
> -----Ursprüngliche 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
>
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