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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> > > [[alternative HTML version deleted]]