Additional file 2.

Supplementary Figure S1: Ziggurat Deconstruction. (a) A hypothetical segmented chromosome (green line) is deconstructed with the simplified procedure used by Ziggurat Deconstruction (ZD) to initialize background SCNA rates. Dotted red and blue lines denote the length and amplitude of amplified and deleted SCNAs, respectively, while solid red and blue lines denote the result of merging the SCNA with the closest adjacent segment. (b) The same hypothetical segmented chromosome (green line) is deconstructed using the more flexible procedure of subsequent rounds of ZD. Here, the ZD is performed with respect to up to two basal levels (dotted magenta lines) that are fit to the data, allowing for amplified and deleted SCNAs to be superimposed.

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Mermel et al. Genome Biology 2011 12:R41   doi:10.1186/gb-2011-12-4-r41