[BioC] making a cdf environment

[James W. MacDonald]

Moore, Stephen wrote:
> Dear All,
> 
> I have been attempting to create a cdf environment that I can use in
> conjunction with the Affy package in R.  I downloaded the makecdfenv
> package and installed it.  I have tried this package in two ways:
> 
> First I tried creating a cdf environment - myname = make.cdf.env("cdf
> file name.cdf")

'myname' is certainly not the correct name for the cdfenv. This is 
important, because the affy package will be looking for a particular 
environment, and if the name isn't correct, will look to the BioC 
website. To get the correct name, you can use the cleancdfname() 
function in the affy package:

cleancdfname("name of the cdf file without the suffix")

Then use that name here:

thenamefromabove <- make.cdf.env("name of the cdf.cdf")

Or another way:

cdfname <- list.files(pattern = "\\.[Cc][Dd][Ff]$")
assign(cleancdfname(sub("\\.[Cc][Dd][Ff]$", "", cdfname)), 
make.cdf.env(cdfname))

> 
> This seemed to work O.K. however, when in the same session I loaded
> the Affy package it couldn't locate this environment.  I though that
> perhaps because I had renamed the actual cdf file name with one of my
> own that this was the problem, so I used the 'cat' argument (perhaps
> wrongly?) as follows:
> 
> 
>> cat ("proper cdf file name is", cleancdfname("my cdf name"), "\n")
> 
> 
> and got the response "proper cdf file name is my cdf file name".
> Again I loaded the affy package and again it failed to find the
> environment.  Exasperated I tried creating a cdf package which I am
> still in the process of doing as follows:
> 
> 
>> make.cdf.package("cdf filename.cdf")
> 
> 
> This again seems to have worked O.K. and has created a subdirectory
> in my working directory with the cdf file name (as required).
> However, I have created this on a windows environment and it says in
> the vignette that I need the source package installation files and
> Perl.  This is where I have come unstuck!  Can anyone give me any
> ideas as to how I might carry on with this, or alternatively how I
> might work with the environment rather that create the package?

Well, installing packages on windows is not completely trivial, but it 
is not rocket science either. If you follow the instructions here:

http://www.murdoch-sutherland.com/Rtools/

you should be able to make the package and go on from there. This is 
probably the preferred solution anyway, since the environment will 
either have to be saved in an .Rdata file that you will have to load 
every time you want to use it, or re-built each time.

HTH,

Jim


> 
> Many Thanks for your time and patience, any help is greatly
> appreciated.
> 
> Stephen.
> 
> Dr. Stephen Moore ArraDx Ltd. Craigavon N. Ireland.
> 
> 
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> 
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-- 
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