pairwise.mod.t.test {MKomics}

Pairwise Moderated t-Tests

Description

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

Usage

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

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.

Value

A data.frame with the results.

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

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)