Hey,

You wish to remove them from the normalised dataset within R, I presume? If the data has been processed by the affy package, then this should work:

#Get the control probe indices
ControlProbes <- grep("^AFFX", featureNames(NormalisedData))

ControlProbes

#Remove the control probes
NormalisedData <- NormalisedData[-ControlProbes,]

#Fit the linear model
fit <- lmFit(NormalisedData, design=DesignMatrix)

You should download the library information for your chip type from Affymetrix / Thermo-Fisher, though, which would give a more detailed description of control probes and their IDs on your chip type. Usually, they begin with AFFX, though.

Let me know if this works.