making a cdf file for expression analysis on a tiling array
1
0
Entering edit mode
Ivan Baxter ▴ 60
@ivan-baxter-1399
Last seen 9.5 years ago
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
cdf affy makecdfenv cdf affy makecdfenv • 1.0k views
ADD COMMENT
0
Entering edit mode
@sean-davis-490
Last seen 10 weeks ago
United States
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
ADD COMMENT

Login before adding your answer.

Traffic: 655 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6