To account for multiple substitutions, we applied the Poisson correction to the proportion of differences x/ n to obtain a distance d for that column: Per-residue amino acid contact density was defined as the number of other residues within 4 Å of the site of interest (Toft and Fares 2010).
As a quantitative measure of the amount of correction, I computed the proportion of the initial direction error corrected by each hand.
The correction rates, the proportion of error corrected by each hand, were calculated with a linear regression model of the online correction of the left and right hands as a function of the initial direction error of each hand in that trial: (3) [ c L c R ] n = [ C L C L R C R L C R ] [ y L y R ] n.
In our sub-group analysis of patients who had experienced vision correction post-surgery, the proportion of patients reaching the MCID and MDC thresholds was only slightly higher than in the overall 'both eyes' cohort.
The correction further reduced the proportion of SNPs in LD (Fig. 2b), which dropped down to 3.4 % for LD > 0.10 and to 1.43 % for LD > 0.25, corresponding to a reduction of 46 and 40%% respectively.
We used the chi-square test with Yates' correction to compare the proportion of regularly-attending adults eligible for the schemes who were estimated as needing treatments, with the proportion of adults who used the schemes that were provided with these treatments.
To measure the improvement of biological signal detection, we applied ANOVA test for differentially methylated CpGs between case and control of Dataset 2 and prostate cancer and normal prostate for Dataset 3 before and after normalization and EB correction and recorded the proportion of CpGs associated with these outcome variables (p value < 0.01 among all analyzed CpGs).
The individual data sets were also subjected to NJ implemented in PAUP using GTR model corrections with the proportion of variable sites and gamma shape estimated from Modeltest 3.7 (Posada 2006).
Although lower estimates were obtained after the use of the correction algorithms, the proportions relative to the different categories remained approximately the same.
The wavy growth of the proportion of synonymous substitutions implies biases in the published correction of the mtDNA clock, which assumed a monotonic growth curve [15].
