Grow an unpruned classification or regression tree (CART) for each bootstrap sample as below.
Thus, following the approach of Tajima's (1996) work, we obtain the probability (p i ) of a particular cytosine site exclusively methylated or exclusively unmethylated in the sample as below: (1) p i = Γ (2 θ m ) Γ (θ m + n ) Γ (θ m ) Γ (2 θ m + n ).
Pearson's product moment correlation coefficient (r) was calculated for CT or ΔCT values of sample pairs as below and plotted on the Signal Correlation Plot and Scatter Plot respectively.
Group A samples were classified as "below 48 copies/ml" for those with an observable amplification of virus during quantitation and Group B were classified as "nondetected" for those for whom no amplification was detected.
When the density of cells in the dish was closed to 70%, cells were harvested for extraction of proteins, mRNA, and DNA samples as described below.
Five hamsters from each group (up to 10 for the placebo groups) were sacrificed on day 7 of infection and sera were collected for assaying alanine aminotransferase activity and virus titers were determined for both liver and serum samples as described below.
GFP fluorescence measurements were also performed for these samples as described below.
We next compared the quantitative data on mRNA copy numbers among samples as described below.
This trough was used for collection of serial water samples as described below.
Finally, we called SNPs for all 62 samples as explained below.
