R/Bioconductor CDF to Affymetrix CDF
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Benjamin Otto ▴ 830
@benjamin-otto-1519
Last seen 8.2 years ago
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? 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 ___________________________________________ -------------- next part -------------- -- 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
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@james-w-macdonald-5106
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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 gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): > > Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg > > Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@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]]
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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
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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
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@benjamin-otto-4909
Last seen 8.2 years ago
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? 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
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