
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$Res <- unclass(results)    tab$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
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