Thanks very much Jenny, now it works!!! Finally the steps are as follows: library(hgu95av2cdf) my.env<-get("hgu95av2cdf") # get the CDF as an environment difference=setdiff(ls(my.env),interestingGenes) #Get all genes that are not in the interesting genes set rm(list=difference, envir=my.env) #Remove the genes for the cdf environment -> the cdf will have only the interesting genes eset<-vsnrma(Dilution) #Performs VSNRMA normalization using only the interesting genes detach("package:hgu95av2cdf") # Remove the modified cdf environment Regards, Javier Jenny Drnevich escribi?: > Hi Javier, > > There are some problems in your codes: > > library("affydata") >> data(Dilution) #Get Dilution data >> cleancdfname("HG_U95Av2") #Get hgu95av2cdf > > This is not actually loading the hgu95av2cdf environment; all it's > doing is converting one text string into another text string. To load > the environment, you would need to do: > > >library(hgu95av2cdf) > >> difference=setdiff(ls(hgu95av2cdf),interestingGenes) #Get all genes >> that are not in the interesting genes set >> rm(list=difference, envir=hgu95av2cdf) #Remove the genes for the cdf >> environment -> the cdf will have only the interesting genes >> data(Dilution) #Get again the data with the updated CDF -> Dilution >> will have only the interesting genes > > You don't need to call the Dilution data set again. Changing the cdf > environment does not affect the data in the Dilution object, just what > it maps to. > >> eset<-vsnrma(Dilution) #Performs normalization using only the >> interesting genes >> detach("package:hgu95av2cdf") # Remove the modified cdf >> >> BUT, after this code, I try to get again the original data: >> data(Dilution) #Get Dilution data >> cleancdfname("HG_U95Av2") #Get hgu95av2cdf > > Your error is because this is not loading the hgu95av2cdf environment, > as I said above. > > HTH, > Jenny > >> ls(hgu95av2cdf) >> >> The following error comes up: >> Error in as.environment(pos): no item "hgu95av2cdf" in the search list >> >> My code is in a for loop and I would like to modify the cdf in each >> iteration to select a different subset of data each time. >> >> Any tips? >> Thanks for your help, >> Javier >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at illinois.edu >