moderTestXgrp: Multiple moderated pair-wise t-tests from limma

In wrMisc: Analyze Experimental High-Throughput (Omics) Data

Multiple moderated pair-wise t-tests from limma

Description

Runs all pair-wise combinations of moderated t-tests from package 'limma' on each line of data against 1st group from 'grp'. Note: This function requires the package limma from bioconductor. The limma contrast-matrix has to be read by column, the lines in the contrast-matrix containing '+1' will be compared to the '-1' lines, eg grpA-grpB .

Usage

moderTestXgrp(
  dat,
  grp,
  limmaOutput = TRUE,
  addResults = c("lfdr", "FDR", "Mval", "means"),
  testOrientation = "=",
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

dat	matrix or data.frame with rows for multiple (independent) tests, use ONLY with 2 groups; assumed as log2-data !!!
grp	(factor) describes column-relationship of 'dat' (1st factor is considered as reference -> orientation of M-values !!)
limmaOutput	(logical) return full (or extended) MArrayLM-object from limma or 'FAlSE' for only the (uncorrected) p.values
addResults	(character) types of results to add besides basic limma-output, data are assumed to be log2 ! (eg "lfdr" using fdrtool-package, "FDR" or "BH" for BH-FDR, "BY" for BY-FDR, "bonferroni" for Bonferroni-correction, "qValue" for lfdr by qvalue, "Mval", "means" or "nonMod" for non-moderated test and he equivaent all (other) multiple testing corrections chosen here)
testOrientation	(character) for one-sided test (">","greater" or "<","less"), NOTE : 2nd grp is considered control/reference, '<' will identify grp1 < grp2
silent	(logical) suppress messages
debug	(logical) additional messages for debugging
callFrom	(character) allow easier tracking of message(s) produced

Value

This function returns a limma-type MA-object (list)

See Also

moderTest2grp for single comparisons, lmFit and the eBayes-family of functions in package limma

Examples

grp <- factor(rep(LETTERS[c(3,1,4)],c(2,3,3)))
set.seed(2017); t8 <- matrix(round(rnorm(208*8,10,0.4),2), ncol=8,
  dimnames=list(paste(letters[],rep(1:8,each=26),sep=""), paste(grp,c(1:2,1:3,1:3),sep="")))
t8[3:6,1:2] <- t8[3:6,1:2] +3                    # augment lines 3:6 (c-f) 
t8[5:8,c(1:2,6:8)] <- t8[5:8,c(1:2,6:8)] -1.5    # lower lines 
t8[6:7,3:5] <- t8[6:7,3:5] +2.2                  # augment lines 
## expect to find C/A in c,d,g, (h)
## expect to find C/D in c,d,e,f
## expect to find A/D in f,g,(h) 
test8 <- moderTestXgrp(t8, grp) 
# If you have limma installed we can now see further
if("list" %in% mode(test8)) head(test8$p.value, n=8)

wrMisc documentation built on Nov. 17, 2023, 5:09 p.m.