5.9 years ago by
N.B., the R packages I reference below are available on Bioconductor.
I happen to have been comparing some human 450k samples to mouse RRBS samples recently, so perhaps I can provide some guidance.
anno <- get450k()
GRanges object now contains a convenient annotation of each probe on the array and the CpG that it should be informative about. I can also recommend the
minfi package, which facilitates a lot of the raw file processing.
Regarding incorporating the MeDIP-seq dataset, that's a little tougher. One possibility is to simply correlate the methylation in the two files. This can be conveniently done by creating a
GRanges object from the MeDIP-seq file and then using
findOverlaps() to get overlapping CpGs from the 450k array. You would then need to get average (or median) methylation of the probes for each of the overlapped regions and then you can plot/calculate the correlation. How well they're correlated remains to be seen. I've generally been unimpressed with MeDIP-seq (we do mostly bisulfite sequencing).