Using minfi, I created the following control strip plot and beta density plot. My data set is on Illumina's EPIC platform.
For the control strip plot on the left, by default, each of the control probe types (e.g bisulfite conversion I, conversion, extension, etc) will have its own plot. Each row represents a sample and each red and green point represents the unmethylated and methylated signal intensity, respectively, for a probe of that control type. My understanding is that a good result is when the distribution of values for each of those control probes are similar between red and green points. This indicates that there are no biases that result in the unmethylated or methylated signal being more readily detected than the other. Is this the correct interpretation? If that is the case, then I seem to have some bias because the methylated data points seem to have a greater intensity than the unmethylated points. This control strip plot was for the hybridization control probes.
Regarding the density plot on the right, I noticed that there seem to be two peaks at the lower end. A beta-value at ~0 and another one at ~0.1. What are some possible explanations of this extra peak?