[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.
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