HI Daren,

Actually, after requests from many of us who do want the all the 
results from topTable to use in R (and not just written out to a file 
using write.fit), Gordon kindly made some changes to the newest 
version of limma out with R 2.8.0 (currently limma_2.16.3). Here's a 
snippet from the help file:

Toptable output for all probes in original (unsorted) order can be 
obtained by topTable(fit,sort="none",n=Inf). However 
<mk:@MSITStore:C:\PROGRA~1\R\R-28~1.0\library\limma\chtml\limma.chm::/writefit.html>write.fit 
or write may be preferable if the intention is to write the results 
to a file. A related method is as.data.frame(fit) which coerces an 
MArrayLM object to a data.frame.

However, this will only give the adjusted p-values for one contrast 
at a time, or the over F-stat and adjusted p-values if more than one 
coefficient is given to topTable. You code below may be better if you 
want results for all the coefficients together in one object.

Cheers,
Jenny


At 11:10 PM 11/25/2008, Daren Tan wrote:

>Hope this helps others
>
>After I sent out the earlier email, realized that there is 
>write.fit. My solution is to modify it such that
>
>fit2tablefunction (fit, results = NULL, file, digits = 3, adjust = 
>"none",    sep = "\t", ...){    if (!is(fit, 
>"MArrayLM"))        stop("fit should be an MArrayLM object")    if 
>(!is.null(results) && !is(results, 
>"TestResults"))        stop("results should be a TestResults 
>object")    if (is.null(fit$t) || is.null(fit$p.value))        fit 
><- eBayes(fit)    p.value <- as.matrix(fit$p.value)    for (j in 
>1:ncol(p.value)) p.value[, j] <- p.adjust(p.value[,        j], 
>method = adjust)    rn <- function(x, digits = digits) if 
>(is.null(x))        NULL    else {        if (is.matrix(x) && 
>ncol(x) == 1)            x <- x[, 1]        round(x, digits = 
>digits)    }    tab <- list()    tab$A <- rn(fit$Amean, digits = 
>digits - 1)    tab$Coef <- rn(fit$coef, digits = digits)    tab$t <- 
>rn(fit$t, digits = digits - 1)    tab$p.value <- rn(p.value, digits 
>= digits + 2)    tab$F <- rn(fit$F, digits = digits - 
>1)    tab$F.p.value <- rn(fit$F.p.value, digits = digits + 
>2)    tab$Res <- uncla!
>  ss(results)    tab$Genes <- fit$genes    return(data.frame(tab, 
> check.names = FALSE))}> From: daren76@hotmail.com> To: 
> bioconductor@stat.math.ethz.ch> Date: Wed, 26 Nov 2008 05:00:01 
> +0000> Subject: [BioC] Limma: how to get same output as topTable 
> but for all the genes ?> > > Apology this question is very general, 
> and no codes to illustrate. How can I emulate topTable to output 
> all the genes, as topTable is not suitable for outputting all 
> genes.> > _______________________________________________> 
> Bioconductor mailing list> Bioconductor@stat.math.ethz.ch> 
> https://stat.ethz.ch/mailman/listinfo/bioconductor> Search the 
> archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>_________________________________________________________________
>
>
>         [[alternative HTML version deleted]]
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor@stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>Search the archives: 
>http://news.gmane.org/gmane.science.biology.informatics.conductor

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich@illinois.edu 
	[[alternative HTML version deleted]]

