Hi everyone,

I found that the annotation from IlluminaHumanMethylation27kanno.ilmn12.hg19 and IlluminaHumanMethylation27kanno.ilmn12.hg19 packages for common CpGs does not match.

data("IlluminaHumanMethylation450kanno.ilmn12.hg19")
data("IlluminaHumanMethylation27kanno.ilmn12.hg19")

ann450k=data.frame(getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19))
ann27k=data.frame(getAnnotation(IlluminaHumanMethylation27kanno.ilmn12.hg19))

head(merge(ann450k,ann27k,by=0))

   Row.names chr.x     pos.x chr.y     pos.y
1 cg00000292 chr16  28890100 chr16  28797601
2 cg00002426  chr3  57743543  chr3  57718583
3 cg00003994  chr7  15725862  chr7  15692387
4 cg00005847  chr2 177029073  chr2 176737319
5 cg00006414  chr7 148822837  chr7 148453770
6 cg00007981 chr11  93862594 chr11  93502242

When looking at Genome Browser, annotation from 27k does not correspond to CpG regions. Using Lifftover tool, I found that IlluminaHumanMethylation27kanno.ilmn12.hg19 coordinates are in fact in hg18 coordinates. I hope this can be corrected, thanks.