Probe filtering beta-values from rgSet

Question

[moldach]

I've see many NA's for beta-values in my rgSet object (either because some probe/CpGs were specifically set NA or because of transformation from intensities to beta-values).

beta <- minfi::getBeta(rgSet)
sumis.na(beta)) # 16,928

I'm trying use the DNAmArray R packages probeFiltering() function to obtain filtered beta-values but I end up getting more missing beta-values which seems odd.

rgSetF <- DNAmArray::probeFiltering(rgSet)
betaF <- minfi::getBeta(rgSetF)
sumis.na(betaF)) # 477,470? Why is there more now?

The rgSet data is ~9Gb so I cannot share it via filedropper but I could probably share it with you via dropbox. I would have to check with my supervisor first but it should be okay if I de-identify samples first. I don't actually know how I would do this to an rgSet object so could someone provided a code example of how to do this please.