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Chunk #90 — 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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Three or less residuals degrees of freedom When there are three or less residual degrees of freedom (number of samples minus number of parameters to estimate), the estimation of the prior variance \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 using the observed variance of logarithmic residuals \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document} $s^{2}_{\text {lr}}$ \end{document}slr2 tends to underestimate \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. In this case, we instead estimate the prior variance through simulation. We match the distribution of logarithmic residuals to a density of simulated logarithmic residuals. These are the logarithm of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document} $\chi ^{2}_{m-p}$ \end{document}χm−p2-distributed random variables added to \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document} $N(0,\sigma _{\text {d}}^{2})$ \end{document}N(0,σd2) random variables to account for the spread due to the prior. The simulated distribution is shifted by − log(m−p) to account for the scaling of the χ2 distribution. We repeat the simulation over a grid of