[BioC] I have trouble using the data from the AnnBuilder Vignette

[John Zhang]

>	Thanks for all of the help. I have apparently, using Jim's
>strategy, obtained the data on the test case.  However, I have had
>difficulty putting the data into a form I can use. I want
>to put all of the data in an Excel speadsheet with each gene
>a row and each data for each gene a column. I have tried
>reading in the library with (library"myPkg") but it doesn't acknowledge
>myPkg's existence.  There is a temporary folder written with the data
>in RDA and XML files, but I have not been able to read them in.

Have you tried to install "myPkg" before loading "myPkg" using library(). 
library(foo) loads foo into R only if foo has already been installed.


>
>	I would greatly appreciate any suggestions.
>
>Thanks and best wishes,
>Rich
>On Nov 15, 2004, at 10:26 PM, James MacDonald wrote:
>
>> If I type
>>
>> perl --version
>>
>> at a command prompt, I get the following
>>
>> This is perl, v5.8.2 built for MSWin32-x86-multi-thread
>> (with 25 registered patches, see perl -V for more detail)
>>
>> Copyright 1987-2003, Larry Wall
>>
>> Binary build 808 provided by ActiveState Corp.
>> http://www.ActiveState.com
>> ActiveState is a division of Sophos.
>> Built Dec  9 2003 10:19:40
>>
>> Perl may be copied only under the terms of either the Artistic License
>> or the
>> GNU General Public License, which may be found in the Perl 5 source 
>> kit.
>>
>> Complete documentation for Perl, including FAQ lists, should be found 
>> on
>> this system using `man perl' or `perldoc perl'.  If you have access to
>> the
>> Internet, point your browser at http://www.perl.com/, the Perl Home
>> Page.
>>
>> As noted in the version information, you can get this port of perl at
>> www.activestate.com.
>>
>> Best,
>>
>> 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
>>>>> Richard Friedman <friedman at cancercenter.columbia.edu> 11/15/04 4:48
>> PM >>>
>> Jim,
>>
>> How do I know if I have that. Otherwise where do I get it?
>>
>> Thanks and best wishes,
>> Rich
>>
>> On Nov 11, 2004, at 7:08 PM, James MacDonald wrote:
>>
>>> I have the ActiveState perl port, which is what you need to build R
>>> libraries from source. If that is what you have then you should be
>>> alright. Note that your path should point to the bin directory of your
>>> perl installation.
>>>
>>> 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
>>>>>> Richard Friedman <friedman at cancercenter.columbia.edu> 11/11/04 4:57
>>> PM >>>
>>> Dear Jim (and John and Everybody):
>>>
>>>
>>> 	What you wrote helps considerably. I have another question
>>> before
>>> I proceed. In your note below, the second  entry in the path file is
>>>
>>> C:\Perl\bin\
>>>
>>> The AnnBuilder documentation states thatit requires Perl to run.
>>> The only Perl I have on my PC is
>>> C:\Documents and Settings\Richard\Local
>>> Settings\Temp\R-2.0.0\share\perl
>>>
>>> Is this sufficient, or do I have to download Perl and place it in a
>>> directory for AnnBuilder to run?
>>>
>>>
>>> Thanks and best wishes,
>>> Rich
>>>
>>>
>>> On Thu, 11 Nov 2004, James W. MacDonald wrote:
>>>
>>>> Richard Friedman wrote:
>>>>> Dear John (and Everyone),
>>>>>
>>>>> 	Thank you very much for your quick reply. I tried what you said,
>>>>> but I got a warrning and an error message but I still can't reachthe
>>>>> object. The warning was that gzip was not found.
>>>>> The error was Error in parseKEGGGenome() : Faild to obtain KEGG
>>> organism
>>>>> code
>>>> You need to download the tool set found here
>>>> (http://www.murdoch-sutherland.com/Rtools/tools.zip ) and make sure
>>> that
>>>> you add the directory where you place the tools to your PATH
>> variable,
>>>> preferably before your windows folder.
>>>>
>>>> In other words, download the tools, unzip in e.g., C:\Rtools, and
>> then
>>>> add this to your PATH by right clicking My Computer -->
>>>> Properties/Advanced/Environment Variables/System variables. Click on
>>> the
>>>> path variable, then the edit button and add C:\Rtools. As an example,
>>> my
>>>> PATH looks like this:
>>>>
>>>> .;C:\Perl\bin\;C:\Rtools;C:\Program
>>>>
>>> Files\TeXLive\bin\win32;C:\WINDOWS\system32;C:\WINDOWS;C:
>>> \WINDOWS\System32\Wbem;c:\mingw\bin;C:\Program
>>>> Files\HTML Help Workshop;C:\Program Files\GNU\WinCvs
>>>> 1.3\CVSNT;C:\Program Files\PuTTY;C:\RW1091\bin;C:\Program
>>>> Files\Subversion\bin
>>>>
>>>> Note that C:\Rtools comes *before* C:\WINDOWS
>>>>
>>>> HTH,
>>>>
>>>> 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
>>>>
>>>
>>> ------------------------------------------------------------
>>> Richard A. Friedman, PhD
>>> Associate Research Scientist
>>> Herbert Irving Comprehensive Cancer Center
>>> Oncoinformatics Core
>>> Lecturer
>>> Department of Biomedical Informatics
>>> Box 95, Room 130BB or P&S 1-420C
>>> Columbia University Medical Center
>>> 630 W. 168th St.
>>> New York, NY 10032
>>> (212)305-6901 (5-6901) (voice)
>>> friedman at cancercenter.columbia.edu
>>> http://cancercenter.columbia.edu/~friedman/
>>>
>>> "That was written by Felix Mendelsohn?
>>> Did he start Mendelsohn's Pizza?"
>>> -Rose Friedman, age 8
>>>
>>>
>>>
>>> **********************************************************
>>> Electronic Mail is not secure, may not be read every day, and should
>>> not be used for urgent or sensitive issues.
>>>
>>>
>> ------------------------------------------------------------
>> Richard A. Friedman, PhD
>> Associate Research Scientist
>> Herbert Irving Comprehensive Cancer Center
>> Oncoinformatics Core
>> Lecturer
>> Department of Biomedical Informatics
>> Box 95, Room 130BB or P&S 1-420C
>> Columbia University Medical Center
>> 630 W. 168th St.
>> New York, NY 10032
>> (212)305-6901 (5-6901) (voice)
>> friedman at cancercenter.columbia.edu
>> http://cancercenter.columbia.edu/~friedman/
>>
>>
>> "That was written by Felix Mendelsohn?
>> Did he start Mendelsohn's Pizza?"
>> -RoseFriedman, age 8
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at 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.
>>
>>
>------------------------------------------------------------
>Richard A. Friedman, PhD
>Associate Research Scientist
>Herbert Irving Comprehensive Cancer Center
>Oncoinformatics Core
>Lecturer
>Department of Biomedical Informatics
>Box 95, Room 130BB or P&S 1-420C
>Columbia University Medical Center
>630 W. 168th St.
>New York, NY 10032
>(212)305-6901 (5-6901) (voice)
>friedman at cancercenter.columbia.edu
>http://cancercenter.columbia.edu/~friedman/
>
>"I agree that Columbia is not monolithic dad.
>'Monolithic' means 'one rock'. There is more
>than one rock at Columbia. There are the different
>bricks in the buildings."- Isaac Friedman, age 14
>

Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084