The whole genome deviation vector, V t0), was sorted from the highest to the lowest standard deviation <img src="http://journals.plos.org/plosone/article/asset?id=info?doi/10.1371/journal.pone.0012116.e008.PNG" class= inline-graphic"/> (see Methods, "Ranking gene ensembles").
After adjustment for population incident risk, the performance of the prediction tools improved; however, on the whole, significant deviations between estimated and observed risk remained.
A sliding window of 200 ms was moved along the signal in steps of 200 ms. Windows with signal standard deviations greater than twice the whole epoch standard deviation were selected for further analysis.
F statistics which include FIT, deviations from Hardy- Weinberg expectation across the whole population, FIS deviation from Hardy- Weinberg expectation within a population and FST, correlation of alleles between subpopulation was calculated using AMOVA approach in Arlequin.
In the case of EnLAG 4, the mainstream goal is to cancel the whole project (maximum deviation).
Thus, the ensemble size of nt = 200, with good resolution, was chosen to evaluate the probability distributions of rv and I for each time point of the gene expression data, { V t0),., V tM }, where V ti) is the whole genome expression deviation vector at ti (i = 0,1,.,12) (see Methods).
In the normal range, the size of shielding box, the electrode location, the deviation between the guarded electrode and the whole electrode center, the deviation between the guard electrode and the unguarded electrode, and the potential of the bolt have little effect on the accuracy.
All (d_{3j}^)'s are the unwanted deviation variables for the goal (i.e., (begin{array}{*{20}c} {M - d_{j} ge 0} & {j = 1,2, ldots,n} end{array})) that make M the maximum deviation, and the whole (d_{3j}^)'s are the wanted deviation variables for the same goal (i.e., (begin{array}{*{20}c} {M - d_{j} ge 0} & {j = 1,2, ldots,n} end{array})) in which all d j deviation variables are unwanted as well.
For the genome-wide correlation analyses, 'variable probes' were identified by calculating an estimate of the standard deviation of the whole data set and then filtering out probes that had a probe-wise standard deviation smaller than the estimated standard deviation.
The motif-preference index that we use is an empirical Z value, i.e., the signed difference between the observed count and the average count; the whole divided by the standard deviation of the count, where both the average and the standard deviation are estimated over the same 1000 randomized sequences mentioned above.
