Streep also included a copy of the book Equal Means Equal by Jessica Neuwirth, president of the ERA Coalition, which calls for women to be given the constitutional right to equality.
Thus, we assume that the copy number data from each individual has been parsed into a collection of putative deletion and amplification intervals, using one of the many algorithms to segment copy number data into intervals of equal copy number (e.g. Chiang et al., 2008; Hupé et al., 2004; Olshen et al., 2004).
Each copy number annotation should define a region of equal copy number: deletion, loss, normal, gain or amplification (Supplementary Table S2).
Oligo and BAC CGH platforms were compared after segmentation into regions of equal copy number as the individual number of copies can be corrupted with noise.
Data were analyzed using circular binary segmentation (CBS) as implemented in the DNA copy R/Bioconductor package [45] with default parameters to translate intensity measurements in regions of equal copy number, each region being defined by at least five consecutive probes.
The traditional approach segments noisy probe-level data in individual tumors (dividing the genome into regions of equal copy number) [11], [12], detects aberrations with a global threshold, and heuristically defines boundaries of regions of frequent change [13], [14].
The aCGH data were analysed using circular binary segmentation [ 45] to translate intensity measurements into regions of equal copy numbers.
Various algorithms for data denoising exist such as the non-parametric method called circular binary segmentation (CBS) [ 15] which splits the chromosomes into regions of equal copy number.
Circular binary segmentation was applied on the ratios using DNAcopy [ 27], available as an R package, to partition the genome into regions of equal copy number.
Using the regions of equal copy numbers produced by CBS, the means of the oligo and BAC segments standard deviations have been computed giving respectively 0.32 and 0.10 confirming the previous result.
