MKmisc (version 1.9)

pairwise.mod.t.test: Pairwise Moderated t-Tests

Description

Performs pairwise moderated t-tests based on Bioconductor package limma.

Usage

pairwise.mod.t.test(x, group, adjust.method = "BH", sort.by = "none")

Value

A data.frame with the results.

Arguments

x

a (non-empty) numeric matrix of data values.

group

an optional factor representing the groups.

adjust.method

see p.adjust

sort.by

see toptable

, where "logFC"

corresponds to difference in means.

Details

The function uses Bioconductor package limma to compute pairwise moderated t-tests. For more details we refer to ebayes.

References

B. Phipson, S. Lee, I.J. Majewski, W.S. Alexander, G.H. Smyth (2016). Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression. Annals of Applied Statistics 10(2), 946-963.

See Also

oneway.test, mod.t.test

Examples

set.seed(123)
X <- rbind(matrix(rnorm(5*20), nrow = 5, ncol = 20),
           matrix(rnorm(5*20, mean = 1), nrow = 5, ncol = 20))
gr <- factor(c(rep("A1", 5), rep("B2", 5), rep("C3", 5), rep("D4", 5)))
mod.oneway.test(X, gr)
pairwise.mod.t.test(X, gr)