Validating Cell Mixture Deconvolution

We describe several examples using existing methylation data sets as benchmarks for validating the proposed method, in order to demonstrate its clinical or epidemiological utility. First we describe the validation data set S₀ used in all examples. Next we describe a laboratory reconstruction experiment, which validates our fundamental proposition that DNA methylation retains substantial information about cell mixtures. Finally we describe the results of applying our methodology to several different target data sets S₁. For the head and neck cancer and ovarian cancer data sets, from which bead chip data were available, a linear mixed effects model with a random intercept for bead chip was used to estimate the corresponding row of B₁. For the remaining data sets, no bead chip data were available; consequently, ordinary least squares was used. 250 bootstrap iterations were used for each example and each of the two bootstrap methods of standard error estimation.