anova.MAList-method {limma} | R Documentation

## ANOVA Table - method

### Description

Analysis of variance method for objects of class `MAList`. Produces an ANOVA table useful for quality assessment by decomposing between and within gene sums of squares for a series of replicate arrays. This method produces a single ANOVA Table rather than one for each gene and is not used to identify differentially expressed genes.

### Usage

`anova(object,design=NULL,ndups=2,...)`

### Arguments

`object`
  object of class `MAList`. Missing values in the M-values are not allowed.
`design`
  numeric matrix containing the design matrix for linear model. The number of rows should agree with the number of columns of M. The number of columns will determine the number of coefficients estimated for each gene.
`ndups`
  number of duplicate spots. Each gene is printed ndups times in adjacent spots on each array.
`...`
  other arguments are not used

### Details

This function aids in quality assessment of microarray data and in the comparison of normalization methodologies.

### Value

An object of class `anova` containing rows for between genes, between arrays, gene x array interaction, and between duplicate with array sums of squares. Variance components are estimated for each source of variation.

### Author(s)

Gordon Smyth

### See Also

`MAList-class`, `bwss.matrix`, `anova`.

An overview of quality assessment and diagnostic functions in LIMMA is given by 6.Diagnostics.

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