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]]

Isaac, The multtest functions withe the test="f" choice works very well on my microarrays (5,000 genes and 48 arrays for 12 factors), also I tried the maanova package from teh jackson lab but gave up because of the difference in the classes and the classical Bioc ones. Susan Holmes Statistics Stanford

Thnaks. I'll try them and check performance. Isaac Robert Gentleman wrote: > The other place that you might look for some interesting things is in > Bob Gray's permax package. > > Robert > > On Wed, Feb 19, 2003 at 10:23:54AM -0800, Susan Holmes wrote: > > > > Isaac, > > The multtest functions withe the test="f" choice > > works very well on my microarrays (5,000 genes > > and 48 arrays for 12 factors), also > > I tried the maanova package from teh jackson lab but gave up because > > of the difference in the classes and the classical Bioc ones. > > > > Susan Holmes > > Statistics > > Stanford > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > -- > +------------------------------------------------------------------- --------+ > | Robert Gentleman phone : (617) 632-5250 | > | Associate Professor fax: (617) 632-2444 | > | Department of Biostatistics office: M1B20 | > | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | > +------------------------------------------------------------------- --------+ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

The other place that you might look for some interesting things is in Bob Gray's permax package. Robert On Wed, Feb 19, 2003 at 10:23:54AM -0800, Susan Holmes wrote: > > Isaac, > The multtest functions withe the test="f" choice > works very well on my microarrays (5,000 genes > and 48 arrays for 12 factors), also > I tried the maanova package from teh jackson lab but gave up because > of the difference in the classes and the classical Bioc ones. > > Susan Holmes > Statistics > Stanford > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+

not (yet) integrated to bioconductor, but it might be what you are looking for: http://www.jax.org/staff/churchill/labsite/software/anova/rmaanova/ind ex.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 >