[BioC] Using CDF file on affylmGUI

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Sat Nov 18 21:17:37 CET 2006

I am not too familiar with the affylmGUI package but I assume it  
builds on the structures from affy. In that case you should be able  
to do it manually:
   you make a cdf environment using "makecdfenv". You can either make  
a package like Jim is saying, which is better in the long run (but  
slightly more complicated especially on windows) or you can just have  
a cdf environment in your workspace. Then you need to link your data  
to this package. Presumably you have read in the data using affy, or  
perhaps using a GUI. Anyway, the data should bve in the form of an  
"AffyBatch" object. Say the data is called something like paulData.  
Then you just do
   R> paulData at cdfName <- "ENVNAME"
with ENVNAME the name of your cdfenv. A slightly more explicit script  
would be something like

R> customCdf <- makecdfenv(...)
R> paulData <- ReadAffy(...)
R> paulData at cdfName <- "customCdf"

check by just doing a
R> paulData
If the cdfName has been set correctly and you have a cdf environment  
in your global workspace, the printing should work without problems.


On Nov 18, 2006, at 3:15 AM, Keith Satterley wrote:

> Hi Paul,
> this feature has been asked for recently. The previous maintainer/ 
> programmer has
> gone some way down this path, but it is not functioning yet. I hope  
> to look at
> this early in December. When it works I'll put it in the devel  
> version of
> Bioconductor and let the list know,
> cheers,
> Keith
> ========================
> Keith Satterley
> Bioinformatics Division
> The Walter and Eliza Hall Institute of Medical Research
> Parkville, Melbourne,
> Victoria, Australia
> ========================
> Paul Christoph Schröder wrote:
>> Dear Bioconductor,
>> I would like to use the affylmGUI but not with a chip from
>> Bioconductor. The problem is, I have my own cdf-file and I want to  
>> use
>> this one instead of the provided by Affymetrix. How should I go on?
>> Many thanks in advance,
>> Best,
>> Paul C. Schröder
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