Hello all, I have a question regarding the annotation of cpgs in the lluminaHumanMethylation450kanno.ilmn12.hg19 library. During my analysis, a cpg with the 'Name' ch.1.xxxxxxxF (where x's are numbers) rather than the normal cgxxxxxxxx. I also happen to get another probe ch.21.xxxxxxR. What do these mean? Why are they named differently? I am having a hard time finding anything online, and any info on what to research would be greatly appreciated!
The probe name indicates the methylation context, which can be either CpG or CpH (or a SNP probe with an rsID).
For example, ch.9.7776528F has hg19 coordinate chr9:7786528. The probe is for a CpH on the forward strand, so that position is a "C" and the next nucleotide is an "A" (H=A, C, or T).
In contrast, cg00000029 is a methylated C in the CpG context with hg19 poistion chr16:53468112, where that nucleotide is a "C" and the next nucleotide is a "G".