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? thanks in advance. Ivan

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