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Global Lowess normalization was used to correct for dye biases, before calculating the log ratios of dye-normalized signals for each feature.
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The null distribution of log likelihood is generated by calculating the log likelihood for each permutation.
For the calculation of Pearson coefficient from log values, data were simply transformed into log before calculating the correlation value.
Expression variance was log transformed before calculating the cubic spline residuals.
For the analysis of change, both baseline and follow-up abnormal white matter were log transformed before calculating the change score.
In the logarithm analysis (P-log), the gene expression data were transformed into logarithmic values before calculating the PCC [see Additional file 6].
Replicates were averaged before calculating the correlation.
Calculate the common logarithm (log) of the number from the previous step.
Because % susA β reaches an asymptote, time (h) was log transformed for the purpose of calculating the slope before used as a fixed variable as well as a random variable to determine the effect of apoJ addition.
Before statistical analysis, these values were converted to the logarithm of the minimal angle of resolution (logMAR) by calculating the base 10 logarithm of the Snellen fraction [e.g. normal = log(20/20) = 0].
Survival rates were calculated using Kaplan-Meier test with p-values calculated using the log rank test.
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