09.Diagnostics

This page gives an overview of the LIMMA functions available for microarray quality assessment and diagnostic plots.

This package provides an <code><a href="/link/anova?package=limma&version=3.28.6&to=limma%3Aanova-method" rd-options="limma:anova-method" data-mini-rdoc="limma:anova-method::anova">anova</a></code> method which is designed for assessing the quality of an array series or of a normalization method.
It is not designed to assess differential expression of individual genes.
<code><a href="/link/anova?package=limma&version=3.28.6&to=limma%3Aanova-method" rd-options="limma:anova-method" data-mini-rdoc="limma:anova-method::anova">anova</a></code> uses utility functions <code><a href="/link/bwss?package=limma&version=3.28.6" rd-options="" data-mini-rdoc="limma::bwss">bwss</a></code> and <code><a href="/link/bwss.matrix?package=limma&version=3.28.6" rd-options="" data-mini-rdoc="limma::bwss.matrix">bwss.matrix</a></code>.

The function <code><a href="/link/arrayWeights?package=limma&version=3.28.6" rd-options="" data-mini-rdoc="limma::arrayWeights">arrayWeights</a></code> estimates the empirical reliability of each array following a linear model fit.

Diagnostic plots can be produced by

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

<code>plotPrintTipLoess</code> uses utility functions <code><a href="/link/gridr?package=limma&version=3.28.6" rd-options="" data-mini-rdoc="limma::gridr">gridr</a></code> and <code><a href="/link/gridc?package=limma&version=3.28.6" rd-options="" data-mini-rdoc="limma::gridc">gridc</a></code>.
<code><a href="/link/plotDensities?package=limma&version=3.28.6" rd-options="" data-mini-rdoc="limma::plotDensities">plotDensities</a></code> uses utility function <code><a href="/link/RG.MA?package=limma&version=3.28.6" rd-options="" data-mini-rdoc="limma::RG.MA">RG.MA</a></code>.

documentation

Data analysis, linear models and differential expression for microarray data.

Gordon Smyth

limma

Linear Models for Microarray Data

09.Diagnostics function

This page gives an overview of the LIMMA functions available for microarray quality assessment and diagnostic plots.

This package provides an <code><a href="anova" rd-options="limma:anova-method">anova</a></code> method which is designed for assessing the quality of an array series or of a normalization method.
It is not designed to assess differential expression of individual genes.
<code><a href="anova" rd-options="limma:anova-method">anova</a></code> uses utility functions <code><a href="bwss" rd-options="">bwss</a></code> and <code><a href="bwss.matrix" rd-options="">bwss.matrix</a></code>.

The function <code><a href="arrayWeights" rd-options="">arrayWeights</a></code> estimates the empirical reliability of each array following a linear model fit.

Diagnostic plots can be produced by

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

<code>plotPrintTipLoess</code> uses utility functions <code><a href="gridr" rd-options="">gridr</a></code> and <code><a href="gridc" rd-options="">gridc</a></code>.
<code><a href="plotDensities" rd-options="">plotDensities</a></code> uses utility function <code><a href="RG.MA" rd-options="">RG.MA</a></code>.

09.Diagnostics: Topic: Diagnostics and Quality Assessment

Description

Arguments

See Also