Thanks a lot, the hint was perfect and I can create a "Ath1121501"-like
list: so I got "a" cdf-file written out, and it can be read-in again with
readCdf...

I have basically used the "tinesath1probe"-information rather than the
"tinesath1cdf" (I assume x and y are the same there)
For the MM-y values I have just added 1 to the PM-y values, the x-values are
for PM and MM the same (at least this is how it seams in the Ath1121501-cdf
list)....
So far, dChip has crashed when reading in the .cdf, but I am going to test
it for other applications and as soon as I have a working file, I'll upload
it to the aroma.affymetrix page...

Thank you a million,

best, Sam

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

> In that case I would obtain the original CDF file from Affymetrix. You can
> use the header of that file as a template. You will also get all the extra
> information of all the probes. You will see that the output is essentially a
> list of lists of lists... and all the re-annotation does is essentially
> re-ordering these lists. That should be easy to figure out. In addition you
> can use the QC probesets from the original CDF files, if you want to include
> them. One thing I would check is whether the same probe occurs in multiple
> probesets - many routines depends on that not being the case - although
> nothing in the CDF specification requires that a probe only belongs to one
> probeset.
>
> Kasper
>
>
> On Oct 27, 2008, at 3:31 , Samuel Wuest wrote:
>
>  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>
>> ------------------------------------------------------
>>
>>       [[alternative HTML version deleted]]
>>
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>>
>>
>
>

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