twoWayAnova: A function for Analysis of Variance
In MKomics: Omics Data Analysis

Description Usage Arguments Details Value Note Author(s) References See Also Examples

This function is a slight modification of function Anova of package genefilter.

1	twoWayAnova(cov1, cov2, interaction, na.rm = TRUE)

`cov1`	The first covariate. It must have length equal to the number of columns of the array that the result of `twoWayAnova` will be applied to.
`cov2`	The second covariate. It must have length equal to the number of columns of the array that the result of `twoWayAnova` will be applied to.
`interaction`	logical, should interaction be considered
`na.rm`	a logical value indicating whether 'NA' values should be stripped before the computation proceeds.

The function returned by twoWayAnova uses lm to fit a linear model of the form lm(x ~ cov1*cov2), where x is the set of gene expressions. The F statistics for the main effects and the interaction are computed and the corresponding p-values are returned.

twoWayAnova returns a function with bindings for cov1 and cov2that will perform a two-way ANOVA.

A first version of this function appeared in package SLmisc.

Matthias Kohl Matthias.Kohl@stamats.de

R. Gentleman, V. Carey, W. Huber and F. Hahne (2006). genefilter: methods for filtering genes from microarray experiments. R package version 1.13.7.

lm, oneWayAnova

set.seed(123)
af1 <- twoWayAnova(c(rep(1,6),rep(2,6)), rep(c(rep(1,3), rep(2,3)), 2))
af2 <- twoWayAnova(c(rep(1,6),rep(2,6)), rep(c(rep(1,3), rep(2,3)), 2), 
                   interaction = FALSE)
x <- matrix(rnorm(12*10), nrow = 10)
apply(x, 1, af1)
apply(x, 1, af2)