MKomics (version 0.7)

mod.oneway.test: Moderated 1-Way ANOVA

Description

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

Usage

mod.oneway.test(x, group, repeated = FALSE, subject, adjust.method = "BH", 
                sort.by = "none")

Arguments

x

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

group

an optional factor representing the groups.

repeated

logical indicating whether there are repeated-measures.

subject

factor with subject IDs; required if repeated = TRUE.

adjust.method

see p.adjust

sort.by

see toptable

Value

A data.frame with the results.

Details

The function uses Bioconductor package limma to compute moderated 1-way ANOVAs. For more details we refer to ebayes.

References

Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43(7), e47.

See Also

oneway.test, mod.t.test

Examples

# NOT RUN {
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

## repeated measures
X <- rbind(matrix(rnorm(6*18), nrow = 6, ncol = 18),
           matrix(rnorm(6*18, mean = 1), nrow = 6, ncol = 18))
gr <- factor(c(rep("T1", 6), rep("T2", 6), rep("T3", 6)))
subjectID <- factor(c(rep(1:6, 3)))
mod.oneway.test(X, gr, repeated = TRUE, subject = subjectID)
# }