[BioC] How to permute the CEL files

[Javier Pérez Florido]

Hello everybody,
I'd like to permutate the values (intensity raw data) of the genes 
within a CEL file of an Affymetrix experiment for using the "new" CEL 
file as a control. The key idea is that I want to keep the order of the 
genes in the chip, but permutate the intensities of the genes, that is, 
asign to each gene contained in the array the intensity of other gene 
selected randomly (if and only if the number of probes is the same). To 
do so, and using only AFFX genes, the code is:

data<-Dilution
dataBackup<-Dilution

->geneNames<-featureNames(data) # Get gene names
->AFFX_genes<-grep("^AFFX",geneNames) # Get positions of AFFX genes
->numArrays<-length(sampleNames(data)) # Num of arrays in the experiment


->for (i in 1:numArrays) #Permutate each array
->{

   ->permutation_AFFX<-sample(1:numAFFX_genes) # Get a permutation for 
AFFX genes

   # Indexes of PMs and MMs probes for AFFX genes
   
->indexes_pm<-indexProbes(data,which="pm",genenames=geneNames[AFFX_genes])
   
->indexes_mm<-indexProbes(data,which="mm",genenames=geneNames[AFFX_genes])
     # Indexes of PMs and MMs probes for the AFFX genes selected randomly
   
->indexes_pm_permutation<-indexProbes(data,which="pm",genenames=geneNames[AFFX_genes[permutation_AFFX]]) 

   
->indexes_mm_permutation<-indexProbes(data,which="mm",genenames=geneNames[AFFX_genes[permutation_AFFX]]) 


    -> for (j in 1:numAFFX_genes)# Change the intensity value of each 
AFFX gene (the intensity value of each probe) using the intensities of 
other AFFX gene selected randomly...
    ->{
       # ...if and only if the number of PM and MM probes for the 
current gene and the one used for permutation is the same
      -> if(length(indexes_pm[[j]])==length(indexes_pm_permutation[[j]]))
      ->{             
intensity(data)[indexes_pm[[j]],i]<-intensity(dataBackup)[indexes_pm_permutation[[j]],i] 
# Assign new intensity to the PM probes
          -> 
intensity(data)[indexes_mm[[j]],i]<-intensity(dataBackup)[indexes_mm_permutation[[j]],i] 
# Assign new intensity to the MM probes
       ->}
->}

The problem is that, this way, it takes so much time to perform the 
operation.
I've also tried using lapply functions, but the are not improvements in 
time. Is there another way of changing the intensities rather than using 
indexProbes and intensity R functions?

Thanks in advance,
Javier