Entering edit mode
Javier Pérez Florido
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840
@javier-perez-florido-3121
Last seen 6.1 years ago
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_gen
es])
->indexes_mm<-indexProbes(data,which="mm",genenames=geneNames[AFFX_gen
es])
# Indexes of PMs and MMs probes for the AFFX genes selected
randomly
->indexes_pm_permutation<-indexProbes(data,which="pm",genenames=geneNa
mes[AFFX_genes[permutation_AFFX]])
->indexes_mm_permutation<-indexProbes(data,which="mm",genenames=geneNa
mes[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_p
ermutation[[j]],i]
# Assign new intensity to the PM probes
->
intensity(data)[indexes_mm[[j]],i]<-intensity(dataBackup)[indexes_mm_p
ermutation[[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
