[BioC] making a cdf file for expression analysis on a tiling array

[Sean Davis]

Ivan Baxter wrote:
> Hi all- I would like to start using the new Arabidopsis Tiling array
> http://www.affymetrix.com/products/arrays/specific/arab_tiling.affx
> for expression studies using bioconductor.   The hurdle I am having 
> trouble with is getting a cdf file to run the makecdfenv package on.   I 
> have downloaded the support package from the Affy website, but I can't 
> find a cdf file in there. Alternatively, I have an R data frame with all 
> the relevant information:
> xposition, yposition, GeneID, etc.   for the array. 
>
> So I am wondering:
> A. Am I just missing the cdf file on Affy's website, or does one of the 
> programs in the library files generate it?
> or
> B. Is there a way that I can make a cdf file from the information I have?
>   

Do you have a BPMAP file?  If so, you might want to consider the oligo 
package.  There are some discussions in the archives about how to use it 
as well as a talk or two online--sorry that I can't find any right this 
minute.

Sean