[BioC] cdf-package to .cdf-file using affxparser

Kasper Daniel Hansen khansen at stat.berkeley.edu
Mon Oct 27 07:49:26 CET 2008

Hi Sam

The easiest way forward would be for you to download a CDF file from  
affymetrix site and use readCdf on that file and then study the output  
of that function. The input structure to writeCdf can be complicated  
at first, but corresponds exactly to the output of readCdf.

Not all information in a CDF file is contained in a CDF package, so  
you cannot always go from package -> file (although often the  
additional information in a CDF file is not used - but that is very  
context dependent).

Why are you interested in doing this? Typically the CDF packages from  
Bioconductor are just packaged versions of the Affy files, so why not  
just use them directly.


On Oct 25, 2008, at 8:09 , Samuel Wuest wrote:

> Dear List,
> I am trying to generate a .cdf-file (that could be used for programs  
> such as
> dChip or aroma.affymetrix) from a cdf-package downloaded from the
> Bioconductor homepage (which provides me an environment containing  
> the probe
> mappings)...
> Is there a direct way to do this (let's say something like
> "writeCdf("myChipcdf-package"))? If not, how can I generate a  
> cdfheader and
> a cdf-list used for the function "writeCdf" from the mappings in the
> environment? (I got hands on a script that uses a flat-file as input  
> for the
> function, but I am having problems generating this flatfile from the R
> environment).
> Thanks a million for any help on this.
> Best wishes,
> Sam
> ------------------------------------------------------
> Wuest Samuel
> Smurfit Institute of Genetics
> Trinity College Dublin
> Dublin 2, Ireland <http://www.tcd.ie/Genetics/wellmer-2/index.html>
> ------------------------------------------------------
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