Dear Kasper,

thanks for your help. I understand that most cdf-packages are packaged
Affy-.cdf files; however, I am using the "tinesath1cdf" package - downloaded
from the Bioconductor homepage, see "experiment data" directory-  which is a
custom-made reannotation of the Ath1-Arabidopsis GeneChip (and according to
the author, no .cdf-file is available). Therefore I was wondering whether
there is a direct way from R-package to .cdf-file.

You have suggested to read-in the affymetrix .cdf-file, now I have done this
already and found that there are some identifiers which are not available in
the custom-made package. However, the probes are mapped all right (I have X,
Y, sequence and probe-set ID) and the identifiers I am missing are basically
arbitrary numbers (e.g. Unit-ids), which I could theoretically just make up
myself: if you do not see any obvious problems there...

Anyway, I ll stick to your suggestion to use the readCdf-output as a
guidline, thanks a million and best wishes,
Sam

2008/10/27 Kasper Daniel Hansen <khansen@stat.berkeley.edu>

> Hi Sam
>
> The easiest way forward would be for you to download a CDF file from
> affymetrix site and use readCdf on that file and then study the output of
> that function. The input structure to writeCdf can be complicated at first,
> but corresponds exactly to the output of readCdf.
>
> Not all information in a CDF file is contained in a CDF package, so you
> cannot always go from package -> file (although often the additional
> information in a CDF file is not used - but that is very context dependent).
>
> Why are you interested in doing this? Typically the CDF packages from
> Bioconductor are just packaged versions of the Affy files, so why not just
> use them directly.
>
> Kasper
>
>
>
> On Oct 25, 2008, at 8:09 , Samuel Wuest wrote:
>
>  Dear List,
>>
>> I am trying to generate a .cdf-file (that could be used for programs such
>> as
>> dChip or aroma.affymetrix) from a cdf-package downloaded from the
>> Bioconductor homepage (which provides me an environment containing the
>> probe
>> mappings)...
>> Is there a direct way to do this (let's say something like
>> "writeCdf("myChipcdf-package"))? If not, how can I generate a cdfheader
>> and
>> a cdf-list used for the function "writeCdf" from the mappings in the
>> environment? (I got hands on a script that uses a flat-file as input for
>> the
>> function, but I am having problems generating this flatfile from the R
>> environment).
>>
>> Thanks a million for any help on this.
>>
>> Best wishes,
>>
>> Sam
>>
>> ------------------------------------------------------
>> Wuest Samuel
>> Smurfit Institute of Genetics
>> Trinity College Dublin
>> Dublin 2, Ireland <http://www.tcd.ie/Genetics/wellmer-2/index.html>
>> ------------------------------------------------------
>>
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>>
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>
>
>

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