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

You will need to use the writeCdf function in the affxparser library. But it is certainly not easy and requires a good understanding of what goes on. I do not know of any specific code examples, but there was a discussion on the list recently with someone who wanted to do this. Briefly, in order to write a CDF file you will need additional information about the design of the chip that is not in the CDF environment. This information is for example related to what base the 13'th base is on so on. The way you get this information is by obtaining the "standard" cdf file from Affy. You should read this into R by using readCdf from affxparser. This gives you the basic information. Now, all you need to do is reorder everything so that new probesets are created (and maybe some probes are left out). This is essentially the information contained in the CDF environment. Kasper On Dec 22, 2008, at 2:46 , shirley zhang wrote: > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >