To follow up on this, FYI: Henrik has made available in his aroma.affymetrix project a function called 'env2Cdf()' that creates a CDF file from an R package/environment. Although I haven't used this specific function, i have used another one to create a CDF from a PdInfo object. http://www.aroma-project.org/node/41 HTH, Guido -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Samuel Wuest Sent: Friday, October 14, 2011 17:32 To: Benjamin Otto Cc: Bioconductor list Subject: Re: [BioC] R/Bioconductor CDF to Affymetrix CDF Hi Benjamin, I would agree with the answer given below, but would like to add that - as far as I recall - a similar post has already been discussed before, https://stat.ethz.ch/pipermail/bioconductor/2008-December/025647.html If you really have to coerce the data into the list-structure that Jim has mentioned, then there are scripts floating around for that already. I have adopted one of these for the ATH1-Arabidopsis array myself, but know that there are some more generic scripts around too. Hope this helps, best, Sam On 14 October 2011 16:17, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Benjamin, > > On 10/14/2011 9:57 AM, Benjamin Otto wrote: >> Dear Colleagues, >> >> has someone an idea how I can convert a CDF file in R/Bioconductor format easily into a Affymetrix (Gene expression console compatible) CDF file format? > I am assuming that this is for a cdf package for which you cannot just > go to netaffx and download? If not, just do that. > > If you cannot just get the CDF from netaffx, then the next question is > for you to define 'easily'. ;-D > > Hypothetically you could use the writeCdf() function in affxparser to > write out a cdf, but you would first have to coerce the data into the > expected format (basically a complex list structure). Doesn't sound > like fun to me. > > Best, > > Jim > > >> >> Best regards >> >> Benjamin >> >> ___________________________________________ >> Benjamin Otto, PhD >> University Medical Center Hamburg-Eppendorf Center for Diagnostics >> Institute For Clinical Chemistry / Central Laboratories Center for >> Internal Medicine I. Department of Internal Medicine Campus Forschung >> N27 Martinistr. 52, >> D-20246 Hamburg >> >> Tel.: +49 40 7410 51908 >> Fax.: +49 40 7410 54971 >> ___________________________________________ >> >> >> >> >> >> >> >> -- >> Pflichtangaben gem?? Gesetz ?ber elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): >> >> Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen >> Rechts; Gerichtsstand: Hamburg >> >> Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des >> Vorsitzenden), Dr. Alexander Kirstein, Joachim Pr?l?, Prof. Dr. Dr. >> Uwe Koch-Gromus >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should > not be used for urgent or sensitive issues > > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- ----------------------------------------------------- Samuel Wuest Smurfit Institute of Genetics Trinity College Dublin Dublin 2, Ireland Phone: +353-1-896 2444 Web: http://www.tcd.ie/Genetics/wellmer-2/index.html Email: wuests at tcd.ie _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor