R: Empirical Bayes shrinkage estimate of sigma^2

sigmashrink {ruv} | R Documentation

## Empirical Bayes shrinkage estimate of sigma^2

### Description

This function (re)implements the empirical bayes shrinkage estimate of Smyth (2004), which is also implemented in the Limma package. This function is normally called from the function `variance_adjust`, and is not normally intended for stand-alone use.

### Usage

    sigmashrink(s2, d)

### Arguments

`s2` | "Standard" estimates of sigma^2
`d` | "Standard" degrees of freedom of the residuals

### Value

A list containing

`sigma2` | Estimates of sigma^2 using the empirical bayes shrinkage method of Smyth (2004)
`df` | Estimate of degrees of freedom using the empirical bayes shrinkage method of Smyth (2004)

### Author(s)

Johann Gagnon-Bartsch johanngb@umich.edu

### References

Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Smyth, 2004.

Using control genes to correct for unwanted variation in microarray data. Gagnon-Bartsch and Speed, 2012. Available at: http://biostatistics.oxfordjournals.org/content/13/3/539.full.

Removing Unwanted Variation from High Dimensional Data with Negative Controls. Gagnon-Bartsch, Jacob, and Speed, 2013. Available at: http://statistics.berkeley.edu/tech-reports/820.

### See Also

`variance_adjust`

[Package ruv version 0.9.6 Index]