R/Intensity.Norm.R

In anapuce: Tools for Microarray Data Analysis

Intensity.Norm <-
  function (fileIN = "resNorm.txt",
            n = 3,
            ind.array = NULL,
            name.A = "A",
            name.M = "M.norm",
            sep = "\t",
            center = FALSE,
            log.transf = TRUE,
            ...)
  {
    if (is.character(fileIN)) {
      res <- read.table(fileIN, header = TRUE, sep = sep, ...)
    } else {
      res <- fileIN
    }
    all.array <-
      sub(name.M, "", names(res)[grep(name.M, names(res))])
    if (is.null(ind.array))
      ind.array <- all.array
    else {
      if (length(setdiff(ind.array, all.array)) != 0)
        cat(paste(name.M, setdiff(ind.array, all.array), sep = ""),
            " not found and not considered \n")
      ind.array <- intersect(ind.array, all.array)
    }
    indA <-
      which(names(res) %in% paste(name.A, ind.array, sep = ""))
    indM <-
      which(names(res) %in% paste(name.M, ind.array, sep = ""))

    if (center) {
      ## Modif parallelisation
      ##MeanArray=apply(as.matrix(res[, indA]),2,mean,na.rm=TRUE)
      MeanArray <- colMeans(as.matrix(res[, indA]), na.rm = TRUE)
      MeanAll = mean(MeanArray)
      A = apply(
        as.matrix(1:length(indA)),
        1,
        FUN = function(x)
          res[, indA[x]] - MeanArray[x] + MeanAll
      )

    } else {
      A = res[, indA]
    }
    ind = rbind(indA, indM)
    Red = apply(
      ind,
      2,
      FUN = function(x)
        (res[, x[1]] + (0.5 * res[, x[2]]))
    )
    Green = apply(
      ind,
      2,
      FUN = function(x)
        (res[, x[1]] - (0.5 * res[, x[2]]))
    )
    if (log.transf)
      Int = data.frame(res[, 1:n], Red, Green)
    else
      Int = data.frame(res[, 1:n], 2 ^ (Red), 2 ^ (Green))
    names(Int) = c(
      names(res)[1:n],
      paste("Red.norm", ind.array, sep = ""),
      paste("Green.norm", ind.array, sep = "")
    )

    Int = Int[, c(1:n, match(paste(
      c("Red.norm", "Green.norm"), rep(ind.array, each = 2), sep = ""
    ), names(Int)))]

    invisible(Int)
    # (c) 2007 Institut National de la Recherche Agronomique


  }