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This procedure allows for both increases and decreases in gene expression to be detected using linear models of differential expression.
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Four QTL were detected using Linear Bayes analyses at 1% FDR (Fig. 4), and their effects were estimated separately in the four individual blocks (Table 1) or together in the full model (Table 2, analysis details described in the methods).
Weakly positive correlations were detected using linear regression analyses, though none were statistically significant.
Very weak positive or negative correlations were detected using linear regression analyses, though none of the correlations were statistically significant.
No significant differences could be detected using a linear model.
HPV infections were detected using HPV linear array, and chi-squared tests and linear regression models were used to compare HPV genotypes across racial/ethnic groups by CIN status.
The presence of hepatitis B surface antigens (HBsAg) in serum was detected using EILSA (Linear chemicals. Joaquim Costa, Barcelona, Spain) according to the manufacturer's instructions.
DE genes were detected using a linear model in the R-package Limma [ 38], taking into account OI as a continuous variable and sex as a factor.
Data was normalised by variance stabilizing normalization (VSN; [78]) and differentially expressed genes were detected using the 'Limma' (Linear Models for Microarray Analysis) package [79]; implementing the empirical Bayes linear modelling approach [80].
Numerous significant SNPs that were detected using a general linear model (GLM) were false positives (Global GLM in Additional file 4: Figure S2).
Large-scale brain networks were detected using a multivariate linear discriminant analysis (canonical variates analysis, CVA) that was tuned to fit the data.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com