I would like to get number of beads used to summarize intensity in infinium methylation 450k data and remove intensities based on less than 3 beads.
I can easily get that information using minfi as follows,
nbeads <- assayData(RGset)$NBeads
How can do that in lumi?
Further, I noticed that number of features are different in MethyLumiM and RGChannelSetExtended classes for same data. Why is it so?
RGChannelSetExtended (storageMode: lockedEnvironment)
assayData: 622399 features, 13 samples
element names: Green, GreenSD, NBeads, Red, RedSD
MethyLumiM (storageMode: lockedEnvironment)
assayData: 485512 features, 13 samples
element names: detection, exprs, methylated, unmethylated
I will appreciate for any help here!