\HeaderA{09.Diagnostics}{Diagnostics and Quality Assessment}{09.Diagnostics}
\keyword{documentation}{09.Diagnostics}
\begin{Description}\relax
This page gives an overview of the LIMMA functions available for microarray quality assessment and diagnostic plots.

This package provides an \code{\LinkA{anova}{anova}} 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{\LinkA{anova}{anova}} uses utility functions \code{\LinkA{bwss}{bwss}} and \code{\LinkA{bwss.matrix}{bwss.matrix}}.

The function \code{\LinkA{arrayWeights}{arrayWeights}} estimates the empirical reliability of each array following a linear model fit.

Diagnostic plots can be produced by

\describe{

\item[ \code{\LinkA{imageplot}{imageplot}} ] Produces a spatial picture of any spot-specific measure from an array image. If the log-ratios are plotted, then this produces an in-silico representation of the well known false-color TIFF image of an array.
\code{\LinkA{imageplot3by2}{imageplot3by2}} will write imageplots to files, six plots to a page.

\item[ \code{\LinkA{plotMA}{plotMA}} ] MA-plots.
One of the most useful plots of a two-color array.
\code{\LinkA{plotMA3by2}{plotMA3by2}} will write MA-plots to files, six plots to a page.
\code{\LinkA{mdplot}{mdplot}} can also be useful for comparing two one-channel microarrays.

\item[ \code{\LinkA{plotPrintTipLoess}{plotPrintTipLoess}} ] Produces a grid of MA-plots, one for each print-tip group on an array, together with the corresponding lowess curve.
Intended to help visualize print-tip loess normalization.

\item[ \code{\LinkA{plotPrintorder}{plotPrintorder}} ] For an array, produces a scatter plot of log-ratios or log-intensities by print order.

\item[ \code{\LinkA{plotDensities}{plotDensities}} ] Individual channel densities for one or more arrays.
An essential plot to accompany between array normalization, especially quantile normalization.
}

\code{plotPrintTipLoess} uses utility functions \code{\LinkA{gridr}{gridr}} and \code{\LinkA{gridc}{gridc}}.
\code{\LinkA{plotDensities}{plotDensities}} uses utility function \code{\LinkA{RG.MA}{RG.MA}}.
\end{Description}
\begin{Author}\relax
Gordon Smyth
\end{Author}