\Header{6.Diagnostics}{Diagnostics and Quality Assessment}
\keyword{documentation}{6.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{\Link{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{\Link{anova}} uses utility functions \code{\Link{bwss}} and \code{\Link{bwss.matrix}}.

Diagnostics plots can be produced by \code{\Link{imageplot}}, \code{\Link{plotMA}}, \code{\Link{plotPrintTipLoess}}, \code{\Link{plotPrintorder}} and \code{\Link{plotDensities}}.

\code{plotPrintTipLoess} uses utility functions \code{\Link{gridr}} and \code{\Link{gridc}}.\end{Description}
\begin{Author}\relax
Gordon Smyth
\end{Author}

