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

Samuel Wuest wuests at tcd.ie
Thu Dec 25 18:32:53 CET 2008

Hi Shirley,

I have had a discussion on the very same topic recently, where I
wanted to write a cdf-environment into a .cdf-file... With good help
from Mark, Elisabeth and Kasper I have written a script that somehow
did the job... However, you'll need some informations specific to the
chip you're using, e.g. how many rows and columns it has and how a
list should look like that you pass to the writeCdf-function; the best
is indeed to read in an Affymetrix cdf-file using the affxparser
package and then you can examine the read-in object a bit closer... I
am attaching you my script I have made for a Arabidopsis cdf-file in a
personal email (it should also appear at one point on the
aroma.affymetrix homepage), hope this helps.

Best Sam

2008/12/22 shirley zhang <shirley0818 at gmail.com>:
> 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
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