sigmashrink {ruv}

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 [e-mail]

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