[BioC] Select an affybatch subset prior to normalization

[Jenny Drnevich]

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

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e-mail: drnevich at illinois.edu