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Chunk #100 — Materials and methods — Shrinkage estimation of logarithmic fold changes

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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
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To ensure that the prior width σr will be independent of the choice of base level, the estimates from the quantile matching procedure are averaged for each factor over all possible contrasts of factor levels. When determining the empirical upper quantile, extreme LFC values (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document} $\left |\beta _{\textit {ir}}^{\text {MLE}}\right | > \log (2) \, 10$\end{document}βirMLE>log(2)10, or 10 on the base 2 scale) are excluded.