Rich, Can you tell us a little more. How was your custom CDF file created? It seems like R is not recognizing the file in your directory as a CDF file. I created a custom CDF file recently for the ATH1 chip that removed known 'SFP' probe pairs using the 'altcdfenv' package and a modification of functions in the 'matchprobes' package (provided to me by Holger Schwender after I posted to this list). I eventually got everything running with the new CDF file assigned to my affybatch and I didn't have to go into the CEL files and hand edit the CDF file name on any of the 30 chips. I'll see if I can help after you send a little more info. Rhonda > > I have created a custom CDF file. > > The purpose is to measure the expression of splice > variations. > > I place the file in the same directory as the CEL > files and crank up R and do the usual BIOC > incantation. > > Based on a suggestion offered by the brainiacs at > University of Michigan ( > http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/cdf readme.htm #How_to_use_the_custom_CDF_file:_ > ) > I try something like this ... > > data<-ReadAffy(); > data@cdfName<-"NEW.CDF" > > But subsequent data processing calls attempt to > connect to the internet and get a CDF file from there. > > Obviously, I missing something. > > Anybody got any ideas? > > Please add to any "RTFM" responses a specific FM to > read. > > Thanks! > > Rich > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Sorry Rich, I realize now that you're working with a custom CDF 'file', not with a custom CDF 'environment' which is what I was doing. Good luck, Rhonda > > I have created a custom CDF file. > > The purpose is to measure the expression of splice > variations. > > I place the file in the same directory as the CEL > files and crank up R and do the usual BIOC > incantation. > > Based on a suggestion offered by the brainiacs at > University of Michigan ( > http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/cdf readme.htm #How_to_use_the_custom_CDF_file:_ > ) > I try something like this ... > > data<-ReadAffy(); > data@cdfName<-"NEW.CDF" > > But subsequent data processing calls attempt to > connect to the internet and get a CDF file from there. > > Obviously, I missing something. > > Anybody got any ideas? > > Please add to any "RTFM" responses a specific FM to > read. > > Thanks! > > Rich > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Rhonda, I wrote a program that takes an original text CDF file as a template and writes out my revised "units" (Affyspeak for probesets). The revised units are sets of probes that map to a quality filtered set of transcripts: higher quality transcripts, chimerics stripped, latest Genbank records, etc. A unit (probeset) can get very large and I'm going to try and reuse probes if it's possible (sometimes probes match to mulitple genes). I'm hoping that this will work with RMA but I am concerned about GCRMA since it relies on additional probeset sequence information which is originally available in the "probetab" files provided by Affymetrix. Another possible concern is if Robert Genetlemen is right and I have to change the chipname in the CEL file. This is, of course, a piece of cake with TEXT CEL files. Binary CEL files will require a little more delicate approach: writing a quick hack program to replace the old string. I will certainly check out the altcdfenv package. Again, if anyone has any caveats when dealing with this, pleas let me and everybody else know about it. Rich --- Rhonda DeCook <rdecook@iastate.edu> wrote: > Rich, > > Can you tell us a little more. How was your custom > CDF file created? It seems > like R is not recognizing the file in your directory > as a CDF file. I created > a custom CDF file recently for the ATH1 chip that > removed known 'SFP' probe > pairs using the 'altcdfenv' package and a > modification of functions in > the 'matchprobes' package (provided to me by Holger > Schwender after I posted > to this list). I eventually got everything running > with the new CDF file > assigned to my affybatch and I didn't have to go > into the CEL files and hand > edit the CDF file name on any of the 30 chips. I'll > see if I can help after > you send a little more info. > > Rhonda > > > > > > > I have created a custom CDF file. > > > > The purpose is to measure the expression of splice > > variations. > > > > I place the file in the same directory as the CEL > > files and crank up R and do the usual BIOC > > incantation. > > > > Based on a suggestion offered by the brainiacs at > > University of Michigan ( > > > http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/cdf readme.htm > #How_to_use_the_custom_CDF_file:_ > > ) > > I try something like this ... > > > > data<-ReadAffy(); > > data@cdfName<-"NEW.CDF" > > > > But subsequent data processing calls attempt to > > connect to the internet and get a CDF file from > there. > > > > Obviously, I missing something. > > > > Anybody got any ideas? > > > > Please add to any "RTFM" responses a specific FM > to > > read. > > > > Thanks! > > > > Rich > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > > >