[BioC] ANOVA performance

[Rafael A. Irizarry]

not (yet) integrated to bioconductor, but it might be what you are looking
for:

http://www.jax.org/staff/churchill/labsite/software/anova/rmaanova/index.html

On Wed, 19 Feb 2003, Isaac Neuhaus wrote:

> Is there a recommended package to run ANOVA. The generic functions in R perform
> very poorly with large microarray datasets which preclude us from running
> permutation analyses. (Please note below the way I am implementing it for a
> one-way anova for three levels). Are there plans to implement some code in C
> passing affy objects?
> 
> Isaac
> 
> my.anova <- function(x) {
>  gr <- gl(3,3,9, label=c(1:3))
>  wg <- as.numeric(x)
>  anova(lm(wg ~ gr))
> }
> 
> data <- read.table("file", header=T, sep = "\t", row.names=1)
> res <- array()
> res <- apply(data, 1, my.anova)
> res <- data.frame(res, row.names = row.names(data))
> write.table(res, quote=FALSE, col.names=FALSE, sep="\t", file="fileout")
> 
> 
> file has this format
> A    B    C    D    E    F    G    H    I
> a    x    x    x    x    x    x    x    x    x
> b    x    x    x    x    x    x    x    x    x
> c    x    x    x    x    x    x    x    x    x
> etc.....
> 
> 
> 
> 	[[alternate HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>