On 2014 Nov 27, Martin Aryee commented:

EWASher (Zou J, 2014) is intended to be used in EWAS settings where the primary interest is in identifying localized differentially methylated regions (i.e. DMRs that affect only a small fraction of methylation sites). The results of EWASher should be interpreted with caution in settings where large-scale methylation changes are expected and/or of interest. The method assumes that large-scale changes are caused by cell type composition effects and will effectively remove these changes from consideration. This is useful in many EWAS settings, but the assumption may not hold when studying cancer or differences between tissues. In the cancer dataset used in our paper, for example, we specifically identify site-specific changes that are above and beyond global hypomethylation changes.

On 2014 Nov 27, Martin Aryee commented:

EWASher (Zou J, 2014) is intended to be used in EWAS settings where the primary interest is in identifying localized differentially methylated regions (i.e. DMRs that affect only a small fraction of methylation sites). The results of EWASher should be interpreted with caution in settings where large-scale methylation changes are expected and/or of interest. The method assumes that large-scale changes are caused by cell type composition effects and will effectively remove these changes from consideration. This is useful in many EWAS settings, but the assumption may not hold when studying cancer or differences between tissues. In the cancer dataset used in our paper, for example, we specifically identify site-specific changes that are above and beyond global hypomethylation changes.