R: Estimate Scale Factor in Mixture of t-Distributions

tmixture {limma}

R Documentation

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.

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.

Value

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

Author(s)

Gordon Smyth