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Chunk #88 — Materials and methods — Estimation of dispersions

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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
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To avoid inflation of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document} $\sigma _{\text {d}}^{2}$ \end{document}σd2 due to dispersion outliers (i.e., genes not well captured by this prior; see below), we use a robust estimator for the standard deviation slr of the logarithmic residuals, (8)\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document} $$ s_{\text{lr}} = {\underset{i}{\text{mad}}} \left(\log \alpha^{\text{gw}}_{i} - \log \alpha_{\text{tr}}(\bar\mu_{i})\right), $$ \end{document}slr=madilogαigw−logαtr(μ¯i),