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Correlations between phenotypes were calculated using Spearman's Rho.
Correlations between phenotypes were calculated using AWM columns (standardized SNP effects across traits) and were visualized as a hierarchical tree cluster, in which strong positive and negative correlations are displayed as proximity and distance, respectively.
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Pearson correlations between all phenotypes were calculated in R (R Core Team; http://www.R-project.org).org
Association between haplotypes and the phenotypes were calculated using a score test implemented in the computer program HAPLO.SCORE [32].
Correlation between DT and BD phenotypes was calculated using Stata (Version 11.0; StataCorp, College Station, TZ).
Statistical significance of gene-set scores between the different synovial phenotypes was calculated using the t-test followed by Benjamini-Hochberg correction of P-values [ 29].
In our study, the phenotypes are needed only to validate the benefits of the proposed method and to compare it to the random sample (correlation coefficients between GEBV and the observed phenotypes are calculated).
The better-parent heterosis (Hybrid phenotype – Better-parent phenotype) and % better-parent heterosis ((Hybrid phenotype – Better-parent phenotype)/Better-parent phenotype) was calculated for each trait and hybrid.
The heritability H2 of each phenotype was calculated separately for each treatment over all strains.
Next, a fluorescence phenotype was calculated for each single event corresponding to log FL1.A /log(FSC.A), which corrected for the correlation between fluorescence level and cell size.
To investigate relationships between phenotypes, individual correlations were calculated.
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