makeMAList {wrMisc}

Make MA-List Object

Description

makeMAList extracts sets of data-pairs (like R & G series) and makes MA objects as MA-List object (eg for ratio oriented analysis). The grouping of columns as sets of replicate-measurements is done according to argumnet MAfac. The output is fully compatible to functions of package limma (Bioconductor).

Usage

makeMAList(
  mat,
  MAfac,
  useF = c("R", "G"),
  isLog = TRUE,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

mat

main input matrix

MAfac

(factor) factor orgnaizing columns of 'mat' (if useF contains the default 'R' and 'G', they should also be part of MAfac)

useF

(character) two specific factor-leves of MAfac that will be used/extracted

isLog

(logical) tell if data is already log2 (will be considered when computing M and A values)

silent

(logical) suppress messages

debug

(logical) additional messages for debugging

callFrom

(character) allow easier tracking of messages produced

Details

This function requires Bioconductor package limma being installed.

Value

limma-type "MAList" containing M and A values

See Also

test2factLimma, for creating RG-lists within limma: MA.RG in normalizeWithinArrays

Examples

set.seed(2017); t4 <- matrix(round(runif(40,1,9),2), ncol=4,
  dimnames=list(letters[c(1:5,3:4,6:4)], c("AA1","BB1","AA2","BB2")))
makeMAList(t4, gl(2,2,labels=c("R","G")))