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

[Richard Friedman]

Dear Jim, Robert, John, and Everybody,

	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.

	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
>
> _______________________________________________
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> 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