Fig. 4

EpiSCOPE fluorescence intensity slide positional effect is reduced with preprocessing methods. Infinium green (Cy3 dye) and red (Cy5 dye) fluorescent intensities are formulated into methylated (meth) and unmethylated (unmeth) signals. These meth and unmeth signals are used to calculate β and M values. If the 369 BeadChips in the EpiSCOPE set are grouped by row (R) and column (C) position on the glass slide, there is evidence that the distribution of fluorescent intensities is associated with this position. The position effect diminishes with preprocessing methods. For some between-array methods no variation in mean is observed, as all the BeadChips have had mean fluorescent intensities moderated to be the same