To whom it may concern, I am currently trying the "affy package" in R and I got it (including the widgets) to run and already did the rma.calculations for some "old" Arabidopsis chips we had. I guess the cdf package "agcdf" is made for this chip (~8000 genes) . But most of our chip experiments are done on the "new" Arabidopsis full genome chip, and I could nowhere find the cdf package for this. Can somebody tell me, where I can obtain this cdf package?? Unfortunately the previous thread on this topic in the forum does not answer the question where to get the file from and how to get it to run Thank you very much Sincerely Norman -- -- Norman Warthmann Department of Molecular Biology Max-Planck-Institute for Developmental Biology Spemannstrasse 37-39 D-72076 T?bingen Germany lab-phone +49-(0)7071-601 1405 cell +49-(0)179-206 24 98 lab-fax +49-(0)7071-601 1412 email norman (at) warthmann.com http://naturalvariation.org

If you have the package makecdfenv and the new arabidopsis cdf file you can make your own cdf environment. Unfortunately, Affy doesn't offer a download for most of their cdf files, so if you cannot make your own cdf environment you will have to hope someone else has the cdf file and will do it for you. If nobody offers and you are completely stuck, email me privately and I will give you a way to ftp the cdf file to me and make the package. Jim James W. MacDonald UMCCC Microarray Core Facility 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Norman Warthmann <norman@warthmann.com> 05/07/03 07:32AM >>> To whom it may concern, I am currently trying the "affy package" in R and I got it (including the widgets) to run and already did the rma.calculations for some "old" Arabidopsis chips we had. I guess the cdf package "agcdf" is made for this chip (~8000 genes) . But most of our chip experiments are done on the "new" Arabidopsis full genome chip, and I could nowhere find the cdf package for this. Can somebody tell me, where I can obtain this cdf package?? Unfortunately the previous thread on this topic in the forum does not answer the question where to get the file from and how to get it to run Thank you very much Sincerely Norman -- -- Norman Warthmann Department of Molecular Biology Max-Planck-Institute for Developmental Biology Spemannstrasse 37-39 D-72076 T?bingen Germany lab-phone +49-(0)7071-601 1405 cell +49-(0)179-206 24 98 lab-fax +49-(0)7071-601 1412 email norman (at) warthmann.com http://naturalvariation.org _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor