All, Has anyone already created the cdf environment for Affy's bovine chip? I only see a single thread in the archives regarding this the subject, it was sent on 02/10/05 and indicated that a version might be put up the next day. I am currently unable to find the package, have written to the author directly but the email bounced. Could someone please point me in the right direction if the package does exist?-- *From:* James W. MacDonald (/jmacdon@landfield.com/ <mailto:jmacdon@landfield.com?subject=re:%20%5bbioc%5d%20cdf%20environ ment%20for%20bovine%20affy%20chips&in-reply-="" to="%3C420AADBA.8060203@med.umich.edu%3E">) *Date:* Thu Feb 10 2005 - 01:42:02 EST * *Next message:* Malard, Joel M: "[BioC] CRANrepository is not a repository or some http problem" <7199.html> * *Previous message:* Margaret Gardiner-Garden: "[BioC] cdf environment for bovine Affy chips" <7197.html> * *In reply to:* Margaret Gardiner-Garden: "[BioC] cdf environment for bovine Affy chips" <7197.html> * *Messages sorted by:* [ date ] <date.html#7198> [ thread ] <thread.html#7198> [ subject ] <index.html#7198> [ author ] <author.html#7198> ---------------------------------------------------------------------- -- Margaret Gardiner-Garden wrote: /> Hi, / /> / /> I have been trying to load the cdf environment for the new bovine Affy chips / /> which is not available on the Bioconductor site as yet. I have tried / /> reading the vignettes and the mailing list but unfortunately still can't / /> work out where I am going wrong. / /> / /> I am using R Version 2.0.1 with developmental version of Bioconductor on a / /> Windows XP machine. I downloaded the file bovine_libraryfile.zip from Affy / /> site and put the file bovine.cdf in the same location as the .RData file. / /> / /> Then in makecdfenv library I did following command..... / /> make.cdf.package("bovine.cdf") / /> This seemed to work OK. Says Creating package in C:/Documents and / /> Settings/margar/Desktop/Matthew/bovinecdf / /> [1] "bovinecdf" / At this point you need to install the cdfenv. Unfortunately, this is a bit more difficult to do than simply zipping things up and using the menu. You have three choices here: 1.) Use make.cdf.env, which will make an environment that you can use now, but will only exist in your current workspace. You can save the workspace and use it again, but it isn't portable like a normal package where anytime you open R, you can load it. 2.) Get the tools to make packages on windows http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-install- packages-into-libraries-in-this-version_003f This is moderately tricky, but if you follow all the (semi-terse) instructions _exactly_, you should be OK. 3.) Wait until tomorrow when I can build the env for you. I would already have it on the BioC site, but I was under the impression that it was the new binary format, and we don't yet have the ability to build envs with the binary .cdf files. Jim -- Anjanette Watson PhD University of Vermont Bioinformatics Core 120A Marsh Life Science Burlington, VT 05405 email Anjanette.Watson@uvm.edu phone 802-656-8612 [[alternative HTML version deleted]]

The bovinecdf is available from BioC. > library(reposTools) > install.packages2("bovinecdf") Will get it installed. Note that there are many cdfenvs available that are not posted on the BioC website. There are two ways to see if a particular one is available. 1.) Just try to install as above and see if you get something. 2.) Check the repository yourself: > library(reposTools) > reps <- repositories() Available Repositories: Select By Number, 0 For None 1:CRAN package repository 2:Bioconductor Release 1.5 Source Repository 3:Bioconductor Release 1.5 Windows Repository 4:Bioconductor Devel Repository 5:Bioconductor Devel Repository 6:Bioconductor Data Packages 7:Bioconductor Developmental Data Packages 8:Bioconductor Experimental Data Repository 9:Bioconductor Course Package Repository 10:Bioconductor CDF Environment Repository 11:Bioconductor Probe Data Packages 12:Bioconductor's Omegahat Repository 13:Bioconductor Repository of Jim Lindseys Packages Selection: 10 > reps Repository Information: Repository Listing: Repository: Bioconductor CDF Environment Repository Type: package pkgs vers types [1,] agcdf 1.4.3 Source, Win32 [2,] ath1121501cdf 1.4.3 Source, Win32 [3,] barley1cdf 1.4.3 Source, Win32 [4,] bovinecdf 1.4.8 Source, Win32 [5,] bsubtiliscdf 1.4.3 Source, Win32 [snip] 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 734-647-5623 >>> Anjanette Watson <anjanette.watson@uvm.edu> 04/15/05 3:41 PM >>> All, Has anyone already created the cdf environment for Affy's bovine chip? I only see a single thread in the archives regarding this the subject, it was sent on 02/10/05 and indicated that a version might be put up the next day. I am currently unable to find the package, have written to the author directly but the email bounced. Could someone please point me in the right direction if the package does exist?-- *From:* James W. MacDonald (/jmacdon@landfield.com/ <mailto:jmacdon@landfield.com?subject=re:%20%5bbioc%5d%20cdf%20environ ment%20for%20bovine%20affy%20chips&in-reply-="" to="%3C420AADBA.8060203@med.umich.edu%3E">) *Date:* Thu Feb 10 2005 - 01:42:02 EST * *Next message:* Malard, Joel M: "[BioC] CRANrepository is not a repository or some http problem" <7199.html> * *Previous message:* Margaret Gardiner-Garden: "[BioC] cdf environment for bovine Affy chips" <7197.html> * *In reply to:* Margaret Gardiner-Garden: "[BioC] cdf environment for bovine Affy chips" <7197.html> * *Messages sorted by:* [ date ] <date.html#7198> [ thread ] <thread.html#7198> [ subject ] <index.html#7198> [ author ] <author.html#7198> ---------------------------------------------------------------------- -- Margaret Gardiner-Garden wrote: /> Hi, / /> / /> I have been trying to load the cdf environment for the new bovine Affy chips / /> which is not available on the Bioconductor site as yet. I have tried / /> reading the vignettes and the mailing list but unfortunately still can't / /> work out where I am going wrong. / /> / /> I am using R Version 2.0.1 with developmental version of Bioconductor on a / /> Windows XP machine. I downloaded the file bovine_libraryfile.zip from Affy / /> site and put the file bovine.cdf in the same location as the .RData file. / /> / /> Then in makecdfenv library I did following command..... / /> make.cdf.package("bovine.cdf") / /> This seemed to work OK. Says Creating package in C:/Documents and / /> Settings/margar/Desktop/Matthew/bovinecdf / /> [1] "bovinecdf" / At this point you need to install the cdfenv. Unfortunately, this is a bit more difficult to do than simply zipping things up and using the menu. You have three choices here: 1.) Use make.cdf.env, which will make an environment that you can use now, but will only exist in your current workspace. You can save the workspace and use it again, but it isn't portable like a normal package where anytime you open R, you can load it. 2.) Get the tools to make packages on windows http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-install- packages-into-libraries-in-this-version_003f This is moderately tricky, but if you follow all the (semi-terse) instructions _exactly_, you should be OK. 3.) Wait until tomorrow when I can build the env for you. I would already have it on the BioC site, but I was under the impression that it was the new binary format, and we don't yet have the ability to build envs with the binary .cdf files. Jim -- Anjanette Watson PhD University of Vermont Bioinformatics Core 120A Marsh Life Science Burlington, VT 05405 email Anjanette.Watson@uvm.edu phone 802-656-8612 [[alternative HTML version deleted]] _______________________________________________ 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.