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Push OK to confirm the contrast (and close the contrast dialog) and again to start the ANOVA calculation.

The first time you use MethylationEPIC array, the manifest file needs to be configured and the window like the one in Figure 4 will pop up. First select the second option (Chromosome is in one column and the physical location is in another column). Marker ID is on the first column (Ilmn ID), Chromosome is on the column CHR, while the Physical Position is on the MAPINFO column. Set according to Figure 4 and select Close. This enable Partek Genomics Suite to parse out probe annotation from the manifest file. 

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