tileHMM (version 1.0-7)

shrinkt.st: Calculate 'Shrinkage t' Statistic

Description

Calculate the ‘shrinkage t’ statistic (Opgen-Rhein and Strimmer, 2007).

Usage

shrinkt.st(X, L, h0.mean = 0, ...)

Arguments

X

Data matrix. Rows correspond to variables (probes) and columns to samples.

L

Design vector. Indicating treatment (1) and control (2) samples. If no control samples are given a one sample t test is carried out.

h0.mean

If no control samples are provided the treatment mean is compared to this value in a one sample t test.

...

Further arguments to be passed to and from other methods.

Value

An object of class "shrinkage" containing the test statistics.

References

Opgen-Rhein, R., and K. Strimmer 2007. Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach. Statist. Appl. Genet. Mol. Biol. 6:9. http://www.bepress.com/sagmb/vol6/iss1/art9/

See Also

shrinkt.stat

Examples

## generate some data
X <- matrix(nrow = 100, ncol = 6)
X[ , 1:3] <- apply(X[ , 1:3], 1, rnorm, 
    mean = rnorm(1, mean = 2, sd = 2), sd = rchisq(1, df = 2))
X[ , 4:6] <- apply(X[ , 4:6], 1, rnorm, 
    mean = rnorm(1, mean = 0, sd = 1), sd = rchisq(1, df = 2))
L <- c(1, 1, 1, 2, 2, 2)

## compute shrinkage t statistic
st.stat <- shrinkt.st(X, L)