7.Diagnostics {limma} | R Documentation

## Diagnostics and Quality Assessment

### Description

This page gives an overview of the LIMMA functions available for microarray quality assessment and diagnostic plots.

This package provides an `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. `anova` uses utility functions `bwss` and `bwss.matrix`.

Diagnostics plots can be produced by `imageplot`, `plotMA`, `plotPrintTipLoess`, `plotPrintorder` and `plotDensities`.

`plotPrintTipLoess` uses utility functions `gridr` and `gridc`. `plotDensities` uses utility function `RG.MA`.

### Author(s)

Gordon Smyth

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