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Each likelihood was centered at the actual location of the corresponding stimulus:
Once a raw probability for each likelihood ratio was calculated, we performed Bonferroni corrections to determine significance.
To account for multiple testing, for each likelihood ratio test, we estimated the false discovery rate (FDR) using the qvalue package [ 133] implemented in R [ 134].
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For each dataset, likelihood ratio tests (LRT) for detection of positive selection were examined using M7-M8 and M8a-M8 comparisons.
For each window, likelihood values of the type-N and type-C trees were maximized using PAML [ 22].
For each analysis, likelihood ratio chi-square p-value of less than 0.05 was considered to be significant.
A distance matrix (Additional file 1) was generated for each maximum likelihood gene tree, showing the relative branch lengths between each organism for each particular protein.
For each gene, Likelihood Ratio Tests (LRT) were used to test whether the estimated dN/dS ratio differed significantly from 1 [ 23].
Therefore, we used the simulations to establish the appropriate rejection thresholds for each statistic (likelihood ratio test for LDLA, t-statistic for EMMA, and BF for BayesC) within each scenario.
For each analysis, likelihoods given in the table are average likelihoods for the 100 trees (there was very little difference between trees).
Figure 10 Handclapping-boxing video: (a) frame 30, (b) frame 100, (c) Activity Area of clapping and boxing, (d) likelihood ratio estimated for each pixel, (e) likelihood ratio values for all pixels, handwaving-handclapping video: (f) frame 10, (g) frame 254, (h) Activity Area, (i) likelihood ratio estimated for each pixel, (j) likelihood ratio values for all pixels, used for change detection.
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