Effect of adjustment for estimated cell type proportion
Adjustment for cell type proportion affected results, but the impact was not consistent across the different types of effects studied. Adjustment for batch resulted in a substantially larger number of DMPs (both negative and positive) for infant sex, but reduced the number of DMPs for fake groups (for models where there were DMPs for fake groups effects). For BMI and intervention, the effect of cell type adjustment was mostly but not entirely to produce more DMPs.The effect of cell type adjustment on top probe rankings was fairly modest, although some quite large discrepancies were observed for Overall, adjustment for cell type proportion tended to improve model behaviour regarding spurious results: the number of significantly differentially methylated probes decreased with adjustment for cell type proportion, though they were not always eliminated. The number of differentially methylated probes for infant sex was increased, which may reflect either improvement (greater ability to detect true effects due to removal of noise due to cell type differences) or harm (greater number of spurious effects) depending on whether the extra probes are in fact differentially methylated between males and females; without knowing the true number and identity of DMPs, we cannot be certain. Similarly, adjustment for cell type proportion increased the number of DMPs for BMI effects in BMIQ and SWAN data, in one scenario (BMIQ with Supervised ComBat) by a substantial amount (from 99 to 2017 DMPs) and these are most likely to be false positives.