For a likelihood analysis, we implemented the MtArt matrix in PhyML 3.0 [ 64].
For cluster analysis, we implemented the Neighbour-Joining method and conditions (tree bisection-reconnection branch swapping, 2,000 bootstrap resampling, and maximum trees saved at each step limited to five) specified by Malik et al. [ 23] using PAUP* v4.0b10 [ 53].
To validate our design and analysis, we implement the proposed scheme in TinyOS.
In this meta-analysis, we implemented the random-effects model using the method of DerSimonian & Laird, instead of fixed-effects model, to bring the individual effect-size estimates together, and the estimate of heterogeneity was taken from the Mantel-Haenszel model [15], [16].
For the experimental analysis, we implemented two systems onto the USRP devices and confirmed the accuracy of the RIPS-u over the RIPS-sq.
For the analysis, we implemented a model in SEDPHAT, based on the mass action law with two equivalent sites and mixed EGFP mAb complexes of 1 1 and 2 1 stoichiometry, that fits the isotherms of free and total bound EGFP signal (which is the sum of both complexes) and does not require the distinction in the experimental data between the different stoichiometry complexes.
To simplify the analysis, we implemented a simple parsing algorithm to categorize each mutation description as deleterious, neutral, activating, or uncategorized.
For RNA-seq data analysis, we implemented an in-house pipeline in the Pfizer High Performance Computing environment as shown in Fig. 2.
Because the total analysis time took place over months, we implemented the analysis of QC samples not only for system equilibration and optimization but also as a stability check: for every 10 biological samples, a QC sample was injected, along the full duration of the analyses.
We implemented the analysis in the framework of Soot compiler, and utilized the Weighted PDS Library as the back-end analysis engine.
Since this spot enumeration module is not included in the standard CellProfiler distribution, we implemented the analysis pipeline in the Developer's Version of CellProfiler, running on Matlab 2008a.
