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(DOCX 2 MB) 12284_2013_50_MOESM2_ESM.xlsx Additional file 2: A list of selected markers that were significantly associated with the trait (by using the mixed linear model) has been provided as an additional file.
Association mapping was performed using the mixed linear model approach.
Each pathway SNP set was analysed in ASReml using the mixed linear model described above.
The association analysis was calculated using the mixed linear model (MLM) method [ 76] incorporated into the TASSEL 3.0 software.
Mixed-effect regression analysis was implemented by using the mixed linear model procedure with restricted maximum likelihood (REML) estimation method.
The SNP were analysed in ASReml [ 28] using the mixed linear model described above and the resulting null distribution was expressed as the proportion of significant SNP.
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We used the mixed linear model (MLM) with control of structure (Q) and kinship (K) to avoid spurious associations (Yu et al. 2006).
We used the mixed linear approach (SAS, Procedure MIXED) with transgenic type (crop, F1 hybrid or first-generation backcross) as the fixed treatment effect, PPR as the covariate and block and treatment×block interaction as random effects.
We used the mixed linear approach (SAS, Procedure MIXED) with block and treatment x block interactions as random effects, to investigate whether the phenological and morphological traits which were found to favour hybridization of weedy mothers were transmitted to their offspring.
We used the mixed-linear model (MLM) function that accounts for different levels of relatedness and controls the type I error rates as described by Yu et al. [31].
Statistical analysis of agronomic parameters and biochemical data were carried out using the mixed General Linear Model (GLM) procedure of the SAS statistical package (SAS Institute, Cary, NC), and treatment comparisons were carried out using the Tukey test.
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