In the simulations for Bragg mirror, we used λ BM =700 nm, n 1=1.47, and n 2=2, whereas the number of layer pairs, N L, is varied from 1 to 3. We chose this number of layer pairs to facilitate the analysis, namely, to decrease the number of analyzed modes, since the number of layer pairs directly determines the number of modes.
We chose this number (50%) from our empirical analysis of exon array data in a number of genes.
(We chose this number of simulations to keep the computation time manageable).
The mean number of reads for the NGS dataset was 3000 which is why we chose this number.
We chose this number of genes due, in part, to computational constraints of the coexpression network analysis.
We chose this number because it has been shown that when there are fewer than 10 studies in a meta-analysis the power of funnel plot asymmetry tests is too low to distinguish chance from real asymmetry (Higgins 2011).
We chose this number based on our prior characterization of these networks where we classified genes as hubs or bottlenecks if their degree or betweenness centrality scores, respectively, were statistical outliers [ 17].
Clustering was performed for each chromatin mark in each cell line individually using k-means clustering with number of clusters set to 5. We chose this number both because it generally produced subprofiles that were clearly distinct in shape, and to avoid too much combinatorial variation for the subsequent meta-clustering (see below).
Because 7 is the number most likely to be rolled on two dice (1 chance in every 6 rolls), most casters chose this number as their main, thus leading to the game of craps.[16][17].[16][17]
