I came across the probeFiltering function in DNAmArray package (https://molepi.github.io/DNAmArray_workflow/04_ProbeFiltering.html), which can be used to filter out cross reactive probes, probes with bd detection p value and based on number of beads. I tried using this with my RGChannelset object and got the following error.
Error in probeFiltering(RGSet_nooutbsxy) :
RGset should be of class 'RGChannelSetExtended' in order to perform filtering on number of beads!
Is there a way I can convert my RGChannelSet object to RGChannelSetExtended? I will not be able to create an RGChannelSetExtended using the read.metharray function in minfi as I am using a combination of 450k data and epic data. Is there any other solution to this problem?