[BioC] onvert an already existing CDF environment into a CDF file or CDF package

Kasper Daniel Hansen khansen at stat.berkeley.edu
Mon Dec 22 08:08:12 CET 2008

You will need to use the writeCdf function in the affxparser library.  
But it is certainly not easy and requires a good understanding of what  
goes on. I do not know of any specific code examples, but there was a  
discussion on the list recently with someone who wanted to do this.

Briefly, in order to write a CDF file you will need additional  
information about the design of the chip that is not in the CDF  
environment. This information is for example related to what base the  
13'th base is on so on. The way you get this information is by  
obtaining the "standard" cdf file from Affy. You should read this into  
R by using readCdf from affxparser. This gives you the basic  
information. Now, all you need to do is reorder everything so that new  
probesets are created (and maybe some probes are left out). This is  
essentially the information contained in the CDF environment.


On Dec 22, 2008, at 2:46 , shirley zhang wrote:

> Dear List,
> I tried 'makecdfenv' to make a  CDF package starting from an
> Affy-provided CDF file. Can anybody tell me how to convert an already
> existing CDF environment into a CDF
> file or CDF package in order to be used in aroma.affymetrix package?
> I am very very appreciated If anybody can give a specific example for
> working with Affymetrix Exon Array.
> Thanks,
> Shirley
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

More information about the Bioconductor mailing list