Traditionally, such designs can be analyzed by the generalized linear mixed models (GLMMs).
The estimation of the dispersion parameter will affect the detection of differential genes reported by the generalized linear model.
Genes with an unadjusted p-value < 0.1 for any of the three contrasts as determined by the generalized linear model testing for the effect of health state were input into WGCNA.
"Complex" diseases are, by definition, influenced by multiple causes, both genetic and environmental, and statistical work on the joint action of multiple risk factors has, for more than 40 years, been dominated by the generalized linear model (GLM).
The phenotype values were the coefficients estimated from the strain-by-gene interaction by the generalized linear model, as they include strain contributions to lethality minus the strain effect, the date effect, and other effects of experimental design.
Several unique correction procedures, such as multi-read correction, bias correction and effective length correction, are incorporated only in Cufflinks2 and Cuffdiff2 [ 33]. edgeR, DESeq2 and Cuffdiff2 calculate their p values by the generalized linear model (GLM) likelihood ratio test [ 32], GLM Wald test [ 31] and t-test [ 12], respectively.
Theorem 1 Let F j, n ( t ) for j = 1, …, m be the Bernstein polynomials of degree n such that their coefficients have been produced by solving the generalized linear system (7).
Theorem 2 Suppose that F j, n ( t ) for j = 1, …, m are the Bernstein polynomials of degree n such that their coefficients have been produced by solving the generalized linear system (10).
Data were analyzed using SAS software [ 10] by using the generalized linear model procedure.
In multivariate results, Wilks' Lambda is historically the most widely used test to show the significant results (Munro 2005) by using the generalized linear model procedure of SPSS.
For within-group analysis of P-values for cost and quality of life data, we conducted a comparative analysis by means of the generalized linear models method with Bonferroni multiple comparisons.
