Importantly , the beta value of a genomic segment is independent from its log2 ratio and the two measures can be used to infer the allele specific copy number and the clonality state of each segment of a tumor genome . CLONET alos provides a space transformation from the beta vs log2 ratio to the cnB vs cnA ( Supplementary Notes , Supplementary Fig . 14 ) , where each segment is visualized at coordinates representing the number of copies of allele NanoString assay - We employed a custom NanoString assay for cases without sufficient material for RNA - seq to evaluate for expression of AR signaling genes , TMPRSS2 - ERG fusion transcript , and neuroendocrine associated genes . FFPE samples were cut onto 10μM thick slides , annotated by the study pathologist , and RNA was extracted using the Ambion RecoverAll ™ Total Nucleic Acid Isolation Kit . RNA quality control was performed on the Agilent 2100 Bioanalyzer system by annotating total RNA concentration and percentage of RNA greater than 300 nucleotides ( nt ) in length . For samples with more than 50 % of total RNA greater than 300 nt , 100ng input RNA was used ; for samples with less than 50 % of total RNA greater than 300 nt , the input RNA was proportionally increased according to the level of degradation . Samples were run on the NanoString nCounter ® Analysis System according to the manufacturers directions . Briefly , total RNA was hybridized overnight at 65 ° , then run on the Prep Station at max sensitivity . Cartridges were then scanned on the Digital Analyzer at 555 fields of view . Raw count data was normalized using the nSolver ™ analysis software version 2.0 , which normalizes samples according to positive and negative control probes and the geometric mean of the 6 housekeeping primers .