limma (version 3.28.14)

tmixture: Estimate Scale Factor in Mixture of t-Distributions

Description

These functions estimate the unscaled standard deviation of the true (unobserved) log fold changes for differentially expressed genes. They are used by the functions ebayes and eBayes and are not intended to be called directly by users.

Usage

tmixture.vector(tstat, stdev.unscaled, df, proportion, v0.lim = NULL)
tmixture.matrix(tstat, stdev.unscaled, df, proportion, v0.lim = NULL)

Arguments

tstat

numeric vector or matrix of t-statistics. tmixture.vector assumes a vector while tmixture.matrix assumes a matrix.

stdev.unscaled

numeric vector or matrix, conformal with tstat, containing the unscaled standard deviations of the coefficients used to compute the t-statistics.

df

numeric vector giving the degrees of freedom associated with tstat.

proportion

assumed proportion of genes that are differentially expressed.

v0.lim

numeric vector of length 2 giving the lower and upper limits for the estimated unscaled standard deviations.

Value

Numeric vector, of length equal to the number of columns of tstat, containing estimated v0 values.

Details

The values in each column of tstat are assumed to follow a mixture of an ordinary t-distribution, with mixing proportion 1-proportion, and (v0+v1)/v1 times a t-distribution, with mixing proportion proportion. Here v1 is stdev.unscaled^2 and v0 is the value to be estimated.

See Also

eBayes