Hi,

I am quite new to methylation data analysis. I am using minfi for illumina 450k data analysis. I would appreciate if someone would answer the following question:

 I want to exclude probes with a) detection P-value > 0.01, and b) intensity summarized with < 3 beads. I think this step should be done before any normalization/adjustment of data.  I could not find information about this procedure in the manual. Can somebody point me to where I get get this information, or can give me an example code on doing this  on RGChannelSet object!