Dear List,

I have preprocessed my 450k methylation array data using minfi and have identified differentially methylated probes in my cancer dataset.

I would like to take advantage of the nice position-dependent/gene-focussed methylation heatmaps available in the methyAnalysis package but am unsure as to how to coerce from a minfi Methylset (or a GenomicMethylSet, which might be more appropriate) into the MethyGenoSet class used by MethyAnalysis.

Is there any way to do this?

Oh, and as an aside, is there any progress on directly applying the bumphunter algorithm to the 450k data? I've never managed to find any DMRs using the dmrFinder function in the CHARM package (function reports zero DMRs), so I must be doing something wrong, as I'm sure that they are present within my dataset.


Thanks,

Ed

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