Ken, I successfully created a new CDF environment for the ATH1 chip awhile ago using the altcdfenv package. I'll show you some of the code that worked for me... ## I built my new cdf environment (using a function similar to buildCdfEnv.matchprobes). > alt.cdf.all<-buildCdfEnv.pmids(pm.i.all.new.2, altcdfname="alt.cdf.ath1", abatch=cel.files.30.lines) ## I reassigned the CDF environment of my old affybatch: > cel.files.30.lines@cdfName<-alt.cdf.all@envName > cdfName(cel.files.30.lines) [1] "alt.cdf.ath1" ## I checked that my alt CDF defined the correct subset size of the original 22810 probes: > alt.cdf.object<-wrapCdfEnvAffy(alt.cdf.ath1,712,712,"ath1121501cdf") > print(alt.cdf.object) Instance of class CdfEnvAffy: name : ath1121501cdf chip-type: ath1121501cdf size : 712 x 712 22787 probe set(s) defined. ## I Looked at the intensity values for a specific probeset/gene(all 30 chips). > pm(cel.files.30.lines,gene="262199_at") ## Other functions applied to the affybatch used only my subsetted list of genes defined by the alternative cdf, as I wanted. HTH, Rhonda > I apologize for re-posting..I'd originally posted this as "Can't normalize > with alternative affy CDF environment." > > After some more searching, I think the problem is that once I have a > CdfEnvAffy class object which was made according to the altcdfenvs tutorial, > how do I take that object and convert it into either a CDF package or a CDF > environment that can actually be used with an affybatch object? > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >