[BioC] solicitation for Affy bovine cdf environment

James MacDonald jmacdon at med.umich.edu
Sun Apr 17 02:18:02 CEST 2005

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

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



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
>>> Anjanette Watson <anjanette.watson at uvm.edu> 04/15/05 3:41 PM >>>
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 at landfield.com/ 
<mailto:jmacdon at landfield.com?Subject=Re:%20%5BBioC%5D%20cdf%20environment%20for%20bovine%20Affy%20chips&In-Reply-To=%3C420AADBA.8060203 at med.umich.edu%3E>)

*Date:* Thu Feb 10 2005 - 01:42:02 EST

   * *Next message:* Malard, Joel M: "[BioC] CRANrepository is not a
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   * *In reply to:* Margaret Gardiner-Garden: "[BioC] cdf environment
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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

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.


Anjanette Watson PhD
University of Vermont Bioinformatics Core
120A Marsh Life Science
Burlington, VT 05405
email Anjanette.Watson at uvm.edu
phone 802-656-8612

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