I guess you're referencing detection P values from the array. Try the lumi package for reading in, normalising and filtering probes that don't have a low enough detection P value, the default threshold is 0.01 in the detectionCall function.

This is what I'd usually do to filter out probes that don't pass detection thresholds.

exprs_data <- exprs(lumi.Q)
present_count <- detectionCall(lumi.Q)
normalised_data <- exprs_data[present_count > 0, ]