comp.ebayes {DEDS}R Documentation

Computing Empirical Bayes Statistics for Differential Expression


comp.ebayes returns a function of one argument with bindings for L and proportion. This function accepts a microarray data matrix as its single argment, when evaluated, computes lod-odds (B statistics) and moderated t statistics of differential expression by emprical Bayes shrinkage of the standard error toward a common value.


comp.ebayes(L = NULL, proportion = 0.01)


L A vector of integers corresponding to observation (column) class labels. For k classes, the labels must be integers between 0 and k-1.
proportion A numeric variable specifying the proportion of differential expression.


The function returned by comp.ebayes calculates B statistics and moderated t statistics for each row of the microarray data matrix, with bindings for L and proportion. It interfaces to a C function.


comp.ebayes returns a function (F) with the bindings for L and proportion . The function F when supplied with a microarray data matrix and evaluated will return a matrix of two columns:

t Moderated t statistics
B B statistics (log-odds) of differential expression


Yuanyuan Xiao,,
Jean Yee Hwa Yang,


Lönnstedt, I. and Speed, T. P. (2002). Replicated microarray data. Statistica Sinica 12, 31-46.

Smyth, G. K. (2003). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments.

See Also



X <- matrix(rnorm(1000,0,0.5), nc=10)
L <- rep(0:1,c(5,5))

# genes 1-10 are differentially expressed

# compute B and moderated t statistics, proportion set as 0.01 <- comp.ebayes(L)
ebayes.X <-

# compute B and moderated t statistics, proportion set as 0.1 <- comp.ebayes(L, proportion=0.1)
ebayes.X <-

[Package DEDS version 1.0.3 Index]