Hi,

I feel the chromosome information is wrong in the output of the cpg.annotate command.  Could you check what's wrong here?

> summary(as.factor(myannotation1$CHR))
    1     2     3     4     5     6     7     8     9    10    11    12    13    14    15    16    17    18    19    20    21    22
42574 22058 26433 22341 11025 13725 13642 19542 25338  5492 23128 31441  9671  3814  7618 22991 18327 21993 32644 26330 18874  8843
   23    24
10326   294

> dmrcoutput1 <- dmrcate(myannotation1, lambda=1000, C=2)
> summary(dmrcoutput$input$CHR)
 chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19  chr2 chr20 chr21 chr22  chr3  chr4  chr5  chr6  chr7  chr8  chr9
42574 22058 26433 22341 11025 13725 13642 19542 25338  5492 23128 31441  9671  3814  7618 22991 18327 21993 32644 26330 18874  8843
 chrX  chrY
10326   294

Hi Yuping,

Looks ok to me. Some chromosomes are necessarily probe-enriched on 450K (e.g. chr6 with all those MHC-associated probes) given that they are also enriched for coding loci. Checking against the annotation:

> data("IlluminaHumanMethylation450kanno.ilmn12.hg19")
> sort(table(IlluminaHumanMethylation450kanno.ilmn12.hg19@data$Locations$chr), decreasing = T)

 chr1  chr6  chr2  chr7 chr11 chr17 chr19  chr3 chr12 chr10  chr5 chr16  chr8  chr4 chr15 chr14 chr13  chrX chr20  chr9 chr22 chr18 chr21  chrY 
46857 36611 34810 30017 28794 27879 25521 25159 24539 24388 24327 21969 20950 20464 15259 15078 12285 11232 10379  9861  8552  5922  4243   416 

Cheers,

Tim