[BioC] R/Bioconductor CDF to Affymetrix CDF

[Hooiveld, Guido]

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 at r-project.org [mailto:bioconductor-bounces at 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 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 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