For each of the tested methods, we picked parameter sets with the general goals of predicting unique, polymorphic, well-supported SNPs, given constraints of available sequence and the need to generate markers in certain marker-poor regions.
As the harvest progresses, he says, "different blocks and clones and soils and picking parameters offer grapes with more weight and more bass notes".
Individual sample tandem mass spectrometry spectra were peak listed using Distiller version 2.1.0.0 (http://www.matrixscience.com/distiller.html) software with peak picking parameters set at 1 as for Signal Noise Ratio (SNR) and at 0.3 for Correlation Threshold (CT) for QTRAP 4000 data and at 5 SRN and 0.4 CT for micro QToF data.
Hence, one can pick parameters such that these curves will cross at some point, and thence it will be possible to pick a pair of input levels on either side of the intersection point that will provide mutual specificity.
For the analysis of migration properties of tracked cells, we picked 4 parameters: track length, displacement length, maximum speed and straightness.
Peaklists were generated from the MS/MS raw data using Distiller software (http://www.matrixscience.com/distiller.html, last accessed December 13 , 2012 with peak-picking parameters set at 5 for signal noise ratio and 0.4 for Correlation Threshold (CT).
We calculated the CF for a million candidate parameter sets chosen quasi-randomly, and then we picked the parameter set giving the lowest CF score as our optimal solution for further detailed analysis.
Starting from the initial guess, we ran DE for 200 generations without enforcing any improvement (random walks) and randomly picked a parameter vector from the last generation as a potential starting point.
Based on their results, we picked several parameter settings, which show directional selection and heterozygote disadvantage in two environments, and permitted a stable equilibrium (as shown in figs. 6 and 11 of Geoghegan and Spencer's article).
The optimal magnetic field density considered as the main objective is obtained by picking several parameters and analyzing their effects.
