[BioC] R/Bioconductor CDF to Affymetrix CDF

[Samuel Wuest]

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
>>
>> ___________________________________________
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-- 
-----------------------------------------------------
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