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The likelihood of odds (LOD) scores at the genome-wide significant (5%) and suggestive (10%) levels were determined by 1000 runs of a permutation test [18].
Such stretches have high likelihood of odds (LOD) to contain a predisposing or causative gene.
Genome-wide likelihood of odds (LOD) significance thresholds were established for each trait using permutation testing (α = 0.05, 1000 permutations).
All results with p values <0.001 (likelihood of odds, LOD = 3) were considered as significant marker gene expression associations.
The initial linkage grouping of markers were performed with a likelihood of odds (LOD) threshold score of 3.0 and a maximum genetic distance of 50 cM.
MapManager QTX gives the LRS (likelihood ratio statistic) value to assess the probability of a false positive, where LRS = 4.6 × LOD (likelihood of odds) [ 44].
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log-likelihood of odds.
Empirical thresholds to declare presence of a QTL were obtained using the resampling by permutation method, performing 1,000 iterations for each trait/chromosome combination (log-likelihood of odds (LOD) score of 3).
For the female map, mean recombination fractions and combined likelihoods of odds (LOD) values of markers from self and hybrid groups were used to integrate the separate linkage groups (LG) and produce the final maps.
aMaximum Likelihood Estimate of odds ratio (OR).
An odds ratio (OR) with a 95%% confidence interval was also assessed for this relationship using conditional maximum likelihood estimate of odds ratio.
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