Additional File 1.

Definitions, additional methods, a description of the paired tumor/normal data set, Heat Maps, Segmentation plots and a comparison of raw CN and segmentation results. The file contains: a) A set of definitions for some terms used throughout the text. b) A detailed method for the Affymetrix 250K Sty assay for formalin fixed, paraffin embedded tissue (FFPET) samples. c) Information on the paired tumor/normal data set used. d) References Cited in the Additional file. e) Heat Maps for the (1) in-lab FFPE normals reference, (2) the VN reference based on in-lab FFPE normals data set and (3) VN reference based on HapMap data set. f) Segmentation plots for the (1) in-lab FFPE normals reference, (2) the VN reference based on in-lab FFPE normals data set and (3) VN reference based on HapMap data set. g) A figure showing a comparison of raw CN and segmentation results (Affymetrix 6.0 array) for a renal carcinoma sample on Chr.2 utilizing three different sources of the reference signal.

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Lisovich et al. BMC Medical Genomics 2011 4:14   doi:10.1186/1755-8794-4-14