Limma: how to get same output as topTable but for all the genes ?
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Daren Tan ▴ 180
@daren-tan-3105
Last seen 7.0 years ago

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.

limma toptable • 9.4k views
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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))}
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Jenny Drnevich ★ 2.0k
@jenny-drnevich-2812
Last seen 3 months ago
United States

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 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


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

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The as.data.frame(fit) call mentioned in the help file snippet does collate results for all coefficients in one data frame.

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@gordon-smyth
Last seen 3 hours ago
WEHI, Melbourne, Australia

Actually, topTable() has always been able to output results for all genes if necessary. As Jenny, points out, you could simply use:

tab <- topTable(fit, n=Inf, coef=2)

to get results for all genes for coefficient 2.

If you wanted to create a data.frame with results for all coefficients, you could use:

tab <- as.data.frame(fit)

and your fit2table function is essentially the same as that. There's no need to write you own code to do this stuff. As Jenny's quote shows, there are hints about this in the topTable help page.

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@lindsaynhayes-13285
Last seen 5 weeks ago
United States

This was super useful. I didn't know you could call each of these variables out of the limma fit output. Thanks for sharing.

Lindsay

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