Effect of probe filtering pre-normalisation 
Filtering probes prior to normalisation, compared to filtering after normalisation, led to modest differences in number of DMPs, rankings of probes by logFC and Probe rankings, by logFC and The question of whether probe filtering should be carried out before or after normalisation is one which has received surprisingly little attention in the literature, but our results suggest that it can make a difference to findings in some contexts. In particular there may be a higher risk of spurious findings in pre-filtered data, but there may also be a risk of failing to detect true differences –either any differences, or specifically hypomethylated or hypermethylated loci, depending upon the normalisation method employed.