MKmisc (version 1.9)

mod.oneway.test: Moderated 1-Way ANOVA

Description

Performs moderated 1-Way ANOVAs based on Bioconductor package limma.

Usage

mod.oneway.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 moderated 1-way ANOVAs. 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)

## Welch 1-Way ANOVA (not moderated)
ow.test <- function(x, g){
  res <- oneway.test(x ~ g)
  c(res$statistic, res$p.value)
}
ow.res <- t(apply(X, 1, ow.test, g = gr))
colnames(ow.res) <- c("F", "p.value")
ow.res