[BioC] cdf environment for bovine Affy chips

[James W. MacDonald]

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


> 
> The resulting bovinecdf folder contains 3 folders: one called "Data" with
> files 00Index and bovinecdf.rda; one called "Man" with files bovinecdf.Rd
> and geometry.Rd, and one called "R" with files geometry.R and zzz.R.  There
> are also 3 files Description, Index and Title.
> 
> 
> I zipped the whole bovinecdf folder to make bovinecdf.zip and used the
> install packages from local zip file (pull down menu in windows) which gives
> command
> install.packages(choose.files('',filters=Filters[c('zip','All'),]),
> .libPaths()[1], CRAN = NULL)
> 
> This gives error
> Error in file(file, "r") : unable to open connection
> In addition: Warning messages:
> 1: error -1 in extracting from zip file
> 2: cannot open file `bovinecdf/DESCRIPTION'
> 
> 
> I am wondering how best to install the cdf environment in windows once you
> have made the package.  Any advice would be greatly appreciated.
> 
> Thanks and Regards
> Marg
> 
> Garvan Institute of Medical Research
> Sydney Australia
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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