Hi everyone, I would like to perform the normalization process to a subset of interesting genes in the affybatch object. I know that "rma" function provides a parameter called "subset" to specify a list of probesets to restrict to for all calculations (the other probesets and their probe intensities are ignored). But I would like to select a subset of data for vsnrma or expresso, which haven't got such parameter. I've checked the bioconductor list and read something about modify the cdf environment, so, I've tried to do this (for Dilution experiment): library("affydata") data(Dilution) #Get Dilution data cleancdfname("HG_U95Av2") #Get 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 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 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

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