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A Class Comparison analysis, based on a Two-sample T-test using the random variance model, yielded 1046 probesets differentially expressed between Ing2+/+ and Ing2−/− testes (P<0.001, FDR<0.04).
After normalization and preprocessing, differentially expressed genes were identified using the random variance model based t-test.
Consequently, we obtained results with more power and less variation by using the random variance model corrected standard t-test or ANOVA methodology [ 8].
Univariate analyses were performed comparing each utilised cell line and cell line derivative using a two-sample t-test using the random variance model.
Differentially expressed genes for 4T1 samples relative to 67NR and 168FARN samples were determined separately with the Class Comparison program using the random variance model and a p value of 0.0001.
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We calculated pooled hazard ratios using the random effects inverse variance method.
Study-specific effect sizes were then combined to determine the pooled effect size and its standard error using the random effects inverse-variance technique.
Meta-regression was performed using the random-effects model and tau2 variance was calculated by the method of the residual maximum likelihood.
All analyses were conducted using the random-effects model (inverse of variance method), as we combined studies with different methodological design and assumed that the true effect size varied from study to study [ 29].
The Q statistic with its distribution approximated by the chi-square distribution is widely used not only for testing homogeneity, but perhaps a more widespread and more important use is its application to estimate the random variance component τ in a random effects model.
The significance of the random variance estimates was assessed using the Wald joint chi-squared test [ 27].
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