Hi Kasper and Jim,

I got DMRs on my local PC in reasonable execution time
with this function call and basic output:


dmrs.senzaXY <- bumphunter(myGenomicRatioSet.senzaXY, design=designMatrix,
cutoff=0.99, cutoffQ=0.99, B=100, verbose=TRUE)

[bumphunterEngine] Parallelizing using 2 workers/cores (backend:
doParallelMC, version: 1.0.7).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Performing 100 permutations.
[bumphunterEngine] Computing marginal permutation p-values.
[bumphunterEngine] cutoff: 0.99
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 40696 bumps.
[bumphunterEngine] Computing regions for each permutation.


I don't know if 40696 is again a "crazy" number of putative bumps.
The n samples of the current dataset is 10, probably this influences
the results.
I'm waiting for other samples of the next Illumina chip-array by my
colleagues
in such way to have a dataset with a doubled size, 20-24, and so execute
the next
bumphunter run.

Thanks for the advice, Best

Giovanni

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