We performed 500 runs of the Gibbs sampling algorithm using the training set, and retained the 50 runs having reached the highest likelihood values.
When a bit-plane is not error-free after the maximum number of decoding runs has been reached, the log-likelihood ratios (LLRs) for the bits that are most likely to be erroneous are flipped, after which channel decoding is attempted anew.
Similarly, the combination of a negative result of the QuantiFERON-TB GOLD In-Tube assay with a negative TST scoring reached the lowest negative likelihood ratio of 0.07.
Analyses of models fitting shifts in selection for each lineage, and corresponding null models, ran with five different starting values of K a /K s (0.001, 0.01, 0.1, 1, and 10) to ensure the algorithm reached the global maximum likelihood optimum, rather than a local optimum.
In practice, T is unknown, but different T values (0.2, 0.3, 0.7, 0.8, only showing data for 0.2 and 0.8) were evaluated to reach the maximum likelihood in model (1) explained in Methods Section.
The remaining five primary cultures presented a total of 11 LOH regions that were not detected by CNAG in original tissues because not reaching the LOH likelihood threshold to be classified as statistically significant by the software and thus visualized in the HMM-LOH track.
Trees were burned in until the distribution of topology likelihoods reached the plateau phase.
A given run was considered to have reached convergence once the likelihood scores reached an asymptotic value and the average standard deviation of split frequencies remained <0.01.
Sir David's letter stated that without assurances from the BMA by the 3pm ultimatum, he would advise Mr Hunt that "we would have reached the end of the road in relation to the likelihood of reaching a negotiated settlement".
