sigmashrink function

Empirical Bayes shrinkage estimate of sigma^2

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.

sigmashrink(s2, d)

Arguments

• s2: "Standard" estimates of sigma^2
• d: "Standard" degrees of freedom of the residuals

Returns

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)

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.

Author(s)

Johann Gagnon-Bartsch johanngb@umich.edu

See Also

variance_adjust