[BioC] Select an affybatch subset prior to normalization

[Javier Pérez Florido]

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 escribió:
> 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
>>
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>
> 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
>