I have recently started working with the Illumina 450K methylation dataset and have started with getting my hands on the "minfi" package. I was just trying to understand a few things with methylation and minfi, and just got into a question which i thought of asking here.
In minfi, as we first convert the Red and Green channels into Methylated and Unmethylated signals. This is stored in the object "MSet.raw" with the help of the following code.
MSet.raw <- preprocessRaw(RGset)
And then I just extract the unlogged methylation channels using the functions getMeth() and getUnmeth() as follows (example for one sample and one CpG locus shown below):
> getMeth(MSet.raw)[1:3,1:2] 7766130113_R06C01 7766130113_R05C02 cg00050873 19568 329 cg00212031 1878 332 cg00213748 2113 380 > getUnmeth(MSet.raw)[1:3,1:2] 7766130113_R06C01 7766130113_R05C02 cg00050873 3752 372 cg00212031 10593 208 cg00213748 515 123
Let me consider an example of CpG locus "cg00050873" in the sample "7766130113_R06C01" given above. It has a methylation value of "19568" and unmethylated value of "3752".
So my question is, how can this one CpG locus have 2 values (both Methylated as well as Unmethylated) ? Where do they come from ? I understand there are two bead types or two color readouts (depending on type1/type2 probes), but isn't only one bead/color deciding that (whether its methylated or unmethylated) for a particular GpG locus? So a particular GpG locus can either have a Methylated or an Unmethylated signal, then how does it fall under both the signals?