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CLUMPP v. 1.1.1 [ 26] was applied to avoid the potential effect of generating several distinct solutions for the estimated cluster membership coefficients in spite of identical initial conditions The average cluster membership was calculated using the LargeK Greedy algorithm.
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Similarity coefficients between runs and the average matrix of ancestry membership were calculated using CLUMPP version 1.1 [ 72] and visualized using DISTRUCT software [ 73].
Module Membership (MM) was calculated as the Pearson correlation between each gene's expression and its module eigengene, calculated using Singular Value Decomposition (Alter et al. 2000).
This procedure yielded 34 coexpression modules, for which the strength of module membership for each transcript was calculated by correlating its expression pattern across all samples with each module's first principal component (Oldham et al., 2008).
Fuzzy membership classification of drinking water quality was calculated according to the quality standards (Table 7).
For each model, the probability of nest membership to either chimpanzees or gorillas was calculated as the response variable for each nest.
In Supplementary Tables S10 16, JI was calculated over phenotype membership, ignoring the ranking of the gene sets.
Normalized gene expression level in each library was calculated as: TC membership size in a library/total number of ESTs of the library × 10,000.
Categorical variables (WTO membership/armed conflict) were analysed cross-sectionally and the % of countries for which the event (WTO membership/armed conflict) was present (1) or absent (0) was calculated in 5-year increments.
The significance of the enrichment was calculated using a one-tailed Fisher's Exact Test (cluster membership versus TF enrichment).
The significance of each module was calculated using the WGCNA package based on gene significance (GS) and module membership (MM).
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