tmixture {limma} | R Documentation

## Estimate Scale Factor in Mixture of t-Distributions

### Description

This function estimates the unscaled standard deviation of the log fold change for differentially expressed genes. It is called by the function `ebayes` and is not intended to be called 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
`stdev.unscaled` | numeric matrix conformal with `tstatf` containing the unscaled standard deviations for the coefficient estimators
`df` | numeric vector giving the degrees of freedom associated with `tstat`
`proportion` | assumed proportion of genes which are differentially expressed
`v0.lim` | numeric vector of length 2, assumed lower and upper limits for the estimated unscaled standard deviation

### 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=stdev.unscaled^2` and `v0` is the value to be estimated.

### Value

Numeric vector of length equal to the number of columns of `tstat` and `stdev.unscaled`.

### Author(s)

Gordon Smyth

### See Also

`ebayes`

[Package limma version 2.10.5 Index]