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@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@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@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@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@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@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

> 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@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@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@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@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@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@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

Richard Friedman wrote: > 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. ABPkgBuilder does only what the name implies; it makes a package. You have to then install the package using R CMD INSTALL (from a command prompt) if you then want to be able to do library(myPkg). To go from an installed package to an Excel file may take a bit of work, considering that you will have several environments containing all your annotation data. > > I would greatly appreciate any suggestions. > > Thanks and best wishes, > Rich -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109