Author: James T. Van Leuven; Martina M. Ederer; Katelyn Burleigh; LuAnn Scott; Randall A. Hughes; Vlad Codrea; Andrew D. Ellington; Holly Wichman; Craig Miller
Title: FX174 Attenuation by Whole Genome Codon Deoptimization Document date: 2020_2_11
ID: mpb4fy16_62
Snippet: Noticed that the data points involved in these regressions were not independent and, as such, the p-values were not valid. We accounted for this by simulating 10,000 datasets (using the estimated coefficient of each block and the estimated Gaussian noise parameter, that captures both experimental noise and variation from model expectations). For each simulated dataset, we repeated the regression for each block and combined across blocks to obtain.....
Document: Noticed that the data points involved in these regressions were not independent and, as such, the p-values were not valid. We accounted for this by simulating 10,000 datasets (using the estimated coefficient of each block and the estimated Gaussian noise parameter, that captures both experimental noise and variation from model expectations). For each simulated dataset, we repeated the regression for each block and combined across blocks to obtain a summary P sim . Across 10,000 simulations, this generated the approximate distribution of P when the model is correct. We then located P obs in this distribution and calculated the p-value as the proportion of simulations where P sim < P obs .
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