Dear list,
I am trying to modify the original PM/MM values of a CEL file. The idea is
to permute randomly the PM-MM values for a given CEL file for a control
experiment.
The code which tries to achieve this is the following:

geneNames<-featureNames(Dilution) # Get genenames of data set Dilution
matrix_pm<-pm(Dilution[,1],geneNames) # Get the PM values (working with the
first array)
matrix_mm<-mm(Dilution[,1],geneNames) # Get the MM values
matrix_pmmm<-cbind(matrix_pm,matrix_mm) #Merge in a unique matrix PM and MM
values for a given probe (Column 1->PM, Column 2-> MM)
permutation_probes<-sample(1:nrow(matrix_pmmm)) #Produce a random
permutation of size given by the number of probes
p_matrix_pmmm<-matrix_pmmm[permutation_probes,] # Permute the order of the
probes
matrix_pm[,1]<-p_matrix_pmmm[,1] #Assign to the original PM values the
permutated PM values (the order of the probes is kept, the value is changed)
matrix_mm[,1]<-p_matrix_pmmm[,2] #Assign to the original MM values the
permutated MM values (the order of the probes is kept, the value is changed)
pm(Dilution[,1],geneNames)<-matrix_pm[,1] # Modify the intensities of the PM
values in the original CEL file
mm(Dilution[,1],geneNames)<-matrix_mm[,1]  # Modify the intensities of the
MM values in the original CEL file

In the last two lines, I get the following error
Error en `pm<-`(`*tmp*`, geneNames, value = c(1852, 111, 648.5, 1436.8,  :
  unused argument(s) (c("100_g_at", "1000_at", "1001_at", "1002_f_at",
"1003_s_at", "1004_at", "1005_at"

The error is the same if I try:

pm(Dilution[,1],geneNames)<-matrix_pm # Modify the intensities of the PM
values in the original CEL file
mm(Dilution[,1],geneNames)<-matrix_mm  # Modify the intensities of the MM
values in the original CEL fil


Or if I try:

pm(Dilution[,1])<-matrix_pm
mm(Dilution[,1])<-matrix_mm

The following error comes up:

Error in phenoData(x)[i, , ...] <- phenoData(value)[i, , ..., drop = FALSE]
:
  the argument "i" is absent

Any tips?
Thanks in advance,
Javier

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