Analysis of Array-CGH Data Using the R and Bioconductor Software Suite
Figure 3
Overview of copy number states of chromosome 1 of several hepatocellular samples. Breakpoint detection was performed with GLAD; thresholds for assigning copy number states were and for gain and loss, respectively, 0.6 for amplification, and for homozygous loss. In (a) only states are shown, in (b) states and original log2 ratios are plotted for a selection of samples. In (a) a minimally altered region (MAR) present in 19 of the 34 arrays is indicated by a gray vertical bar. Red indicates loss, green gain, and dark green amplification. Base pair position along chromosome 1 is plotted on the -axis (Mbp scale at the bottom, cytogenetic banding at the top); samples are shown along the -axis.
