toptable {limma}R Documentation

Table of Top Genes from Linear Model Fit

Description

Extract a table of the top-ranked genes from a linear model fit.

Usage

toptable(fit,coef=1,number=10,genelist=NULL,A=NULL,eb=NULL,adjust.method="holm",sort.by="B",resort.by=NULL,...)
topTable(fit,coef=1,number=10,genelist=NULL,adjust.method="holm",sort.by="B",resort.by=NULL)

Arguments

fit list containing a linear model fit produced by lmFit, lm.series, gls.series or rlm.series. For topTable, fit should be an object of class MArrayLM as produced by lmFit.
coef column number or column name specifying which coefficient or contrast of the linear model is of interest
number how many genes to pick out
genelist data frame or character vector containing gene information. If not specified, this will be taken from the genes component of fit.
A matrix of A-values or vector of average A-values.
eb output list from ebayes(fit)
adjust.method method to use to adjust the P-values for multiple testing, e.g., "holm" or "fdr". See p.adjust for the available options. If "none" then the P-values are not adjusted. A NULL value will result in the default adjustment method, which is "holm".
sort.by character string specifying statistic to rank genes by. Possibilities are "M", "A", "T", "P" or "B".
resort.by character string specifying statistic to sort the selected genes by in the output data.frame. Possibilities are "M", "A", "T", "P" or "B".
... any other arguments are passed to ebayes if eb is NULL

Details

This function summarizes a fit object produced by lmFit, lm.series, gls.series or rlm.series by selecting the top-ranked genes for any given contrast.

The sort.by argument is used to select the top genes. Normally the genes appear in order of selection in the output table. If one wants the table to be in some order other than selection order, the resort.by argument may be used. For example, topTable(fit, sort.by="B", resort.by="M") selects the top genes according to log-odds of differential expression and then orders the resulting genes by log-ratio. topTable(fit, sort.by="M", resort.by="M") would select the genes by absolute log-ratio and then sort then by signed log-ratio from must positive to most negative.

Value

A dataframe with a row for the number top genes and the following columns:

genelist if genelist was included as input
M estimate of the effect or the contrast, on the log2 scale
t moderated t-statistic
P.Value nominal P-value
B log odds that the gene is differentially expressed

Author(s)

Gordon Smyth

See Also

ebayes, p.adjust, lm.series, gls.series, rlm.series.

Examples

#  Simulate gene expression data,
#  6 microarrays and 100 genes with first gene differentially expressed
M <- matrix(rnorm(100*6,sd=0.3),100,6)
M[1,1:3] <- M[1,1:3] + 2
#  Design matrix includes two treatments, one for first 3 and one for last 3 arrays
design <- cbind(First3Arrays=c(1,1,1,0,0,0),Last3Arrays=c(0,0,0,1,1,1))
fit <- lm.series(M,design=design)
toptable(fit)

[Package limma version 1.6.7 Index]