Question: Custom CDF Files - howto ?
14.3 years ago by
Rhonda DeCook • 90
Rhonda DeCook • 90 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 >
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