R/ChipEffectSet.STATS.R

In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

setMethodS3("boxplotStats", "ChipEffectSet", function(this, type=c("NUSE", "RLE"), transform=NULL, ...) {
  if (toupper(type) == "NUSE") {
    calculateNuseBoxplotStats(this, ...)
  } else if (toupper(type) == "RLE") {
    calculateRleBoxplotStats(this, ...)
  } else {
    calculateFieldBoxplotStats(this, field=type, transform=transform, ...)
  }
})




setMethodS3("calculateFieldBoxplotStats", "ChipEffectSet", function(this, field=c("theta", "sdTheta"), transform=NULL, arrays=NULL, subset=NULL, ..., merge=FALSE, verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Local functions
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # So that one can call plotRle(qa, show.names=FALSE), i.e. not
  # worry about what arguments are in '...'.
  boxplotStats <- appendVarArgs(boxplot.stats)


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  nbrOfArrays <- length(this)
  cdfMono <- getCdf(this)
  nbrOfUnits <- nbrOfUnits(cdfMono)

  # Argument 'field':
  field <- match.arg(field)

  # Argument 'transform':
  if (is.null(transform)) {
  } else if (is.function(transform)) {
  } else {
    throw("Argument 'transform' is not a function: ", class(transform)[1])
  }


  # Argument 'arrays':
  if (is.null(arrays)) {
    arrays <- seq_len(nbrOfArrays)
  } else {
    arrays <- Arguments$getIndices(arrays, max=nbrOfArrays)
    nbrOfArrays <- length(arrays)
  }

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }

  # Argument 'subset':
  if (!(is.null(subset))) {
    getFraction <- (length(subset) == 1) && (subset >= 0) && (subset < 1)
    if (!getFraction) {
      units <- Arguments$getIndices(subset, max=nbrOfUnits)
    } else {
      units <- identifyCells(cdfMono, indices=subset, verbose=less(verbose))
    }
  } else {
    units <- 1:nbrOfUnits
  }


  # Get the (unit, group, cell) map
  ugcMap <- getUnitGroupCellMap(this, units=units, verbose=less(verbose, 5))

  verbose && enter(verbose, "Calculating '", field,
                  "' statistics for ", nbrOfArrays, " (specified) arrays")
  verbose && cat(verbose, "Using (unit,group,cell) map:")
  verbose && str(verbose, ugcMap)

  # For each file, calculate boxplot statistics
  stats <- list()
  for (kk in seq_along(arrays)) {
    array <- arrays[kk]
    cef <- this[[array]]
    verbose && enter(verbose, sprintf("Array #%d ('%s') of %d",
                                          kk, getName(cef), nbrOfArrays))
    data <- extractMatrix(cef, fields=field, units=ugcMap)
    data <- as.vector(data)
    if (is.function(transform)) {
      data <- transform(data)
    }
    stats[[kk]] <- boxplotStats(data, ...)
    # Not needed anymore
    data <- NULL
    verbose && exit(verbose)
  }
  names(stats) <- getNames(this)[arrays]
  verbose && exit(verbose)

  # Merge boxplot stats?
  if (merge)
    stats <- mergeBoxplotStats(stats)

  attr(stats, "type") <- field
  attr(stats, "transform") <- transform

  stats
}, protected=TRUE) # calculateFieldBoxplotStats()






# ... : additional arguments to bxp().
setMethodS3("calculateRleBoxplotStats", "ChipEffectSet", function(this, arrays=NULL, subset=NULL, ..., merge=FALSE, verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Local functions
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # So that one can call plotRle(qa, show.names=FALSE), i.e. not
  # worry about what arguments are in '...'.
  boxplotStats <- appendVarArgs(boxplot.stats)


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  nbrOfArrays <- length(this)
  cdfMono <- getCdf(this)
  nbrOfUnits <- nbrOfUnits(cdfMono)

  # Argument 'arrays':
  if (is.null(arrays)) {
    arrays <- seq_len(nbrOfArrays)
  } else {
    arrays <- Arguments$getIndices(arrays, max=nbrOfArrays)
    nbrOfArrays <- length(arrays)
  }

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }

  # Argument 'subset':
  if (!(is.null(subset))) {
    getFraction <- (length(subset) == 1) && (subset >= 0) && (subset < 1)
    if (!getFraction) {
      units <- Arguments$getIndices(subset, max=nbrOfUnits)
    } else {
      units <- identifyCells(cdfMono, indices=subset, verbose=less(verbose))
    }
  } else {
    units <- 1:nbrOfUnits
  }


  # Get the (unit, group, cell) map
  ugcMap <- getUnitGroupCellMap(this, units=units, verbose=less(verbose, 5))

  # get the vector of median stdvs
  verbose && enter(verbose, "Calculating average log chip effects")
  # Calculating the average on the log (but stored on the intensity) scale.
  avg <- getAverageLog(this, field="intensities", verbose=verbose)
  verbose && exit(verbose)

  medianLE <- extractMatrix(avg, field="theta", units=ugcMap,
                                                 verbose=less(verbose, 5))
  medianLE <- log2(as.vector(medianLE))
  # Not needed anymore
  avg <- NULL

  verbose && enter(verbose, "Calculating RLE statistics for ", nbrOfArrays,
                                                    " (specified) arrays")
  verbose && cat(verbose, "Using (unit,group,cell) map:")
  verbose && str(verbose, ugcMap)

  # For each file, calculate boxplot statistics
  stats <- list()
  for (kk in seq_along(arrays)) {
    array <- arrays[kk]
    cef <- this[[array]]
    verbose && enter(verbose, sprintf("Array #%d ('%s') of %d",
                                          kk, getName(cef), nbrOfArrays))

    theta <- extractMatrix(cef, field="theta", units=ugcMap,
                                                verbose=less(verbose, 5))
    theta <- log2(as.vector(theta))

    # Sanity check
    if (length(theta) != length(medianLE)) {
      throw("Internal error: The number of 'theta' does not match the number of 'medianLE': ", length(theta), " != ", length(medianLE))
    }

    stats[[kk]] <- boxplotStats(theta-medianLE, ...)
    # Not needed anymore
    theta <- NULL
    verbose && exit(verbose)
  }
  # Not needed anymore
  medianLE <- units <- NULL
  names(stats) <- getNames(this)[arrays]
  verbose && exit(verbose)

  # Merge boxplot stats?
  if (merge)
    stats <- mergeBoxplotStats(stats)

  attr(stats, "type") <- "RLE"

  stats
}, protected=TRUE) # calculateRleBoxplotStats()



setMethodS3("calculateNuseBoxplotStats", "ChipEffectSet", function(this, arrays=NULL, subset=NULL, ..., merge=FALSE, verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  cdfMono <- getCdf(this)
  nbrOfUnits <- nbrOfUnits(cdfMono)
  nbrOfArrays <- length(this)

  # Argument 'arrays':
  if (is.null(arrays)) {
    arrays <- seq_len(nbrOfArrays)
  } else {
    arrays <- Arguments$getIndices(arrays, max=nbrOfArrays)
    nbrOfArrays <- length(arrays)
  }

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }

  # Argument 'subset':
  if (!(is.null(subset))) {
    getFraction <- (length(subset) == 1) && (subset >= 0) && (subset < 1)
    if (!getFraction) {
      units <- Arguments$getIndices(subset, max=nbrOfUnits)
    } else {
      units <- identifyCells(cdfMono, indices=subset, verbose=less(verbose))
    }
  } else {
    units <- 1:nbrOfUnits
  }


  # Get the (unit, group, cell) map
  ugcMap <- getUnitGroupCellMap(this, units=units, verbose=less(verbose, 5))

  # get the vector of median stdvs
  verbose && enter(verbose, "Extracting average standard errors across all arrays in the set")
  # Calculating the average on the log (but stored on the intensity) scale.
  avg <- getAverageLog(this, field="stdvs", verbose=verbose)
  verbose && exit(verbose)

  # Note, the average of the 'stdvs' is stored in the 'theta' field.
  medianSE <- extractMatrix(avg, field="theta", units=ugcMap,
                                                 verbose=less(verbose, 5))
  # Not needed anymore
  avg <- NULL
  medianSE <- log2(as.vector(medianSE))

  verbose && enter(verbose, "Calculating NUSE statistics for ", nbrOfArrays,
                                                    " (specified) arrays")
  verbose && cat(verbose, "Using (unit,group,cell) map:")
  verbose && str(verbose, ugcMap)

  # For each file, calculate boxplot statistics
  stats <- list()
  for (kk in seq_along(arrays)) {
    array <- arrays[kk]
    cef <- this[[array]]
    verbose && enter(verbose, sprintf("Array #%d ('%s') of %d",
                                          kk, getName(cef), nbrOfArrays))
    stdvs <- extractMatrix(cef, field="sdTheta", units=ugcMap,
                                                verbose=less(verbose, 5))
    stdvs <- log2(as.vector(stdvs))

    # Sanity check
    if (length(stdvs) != length(medianSE)) {
      throw("Internal error: The number of 'stdvs' does not match the number of 'medianSE': ", length(stdvs), " != ", length(medianSE))
    }

    stats[[kk]] <- boxplot.stats(stdvs/medianSE, ...)
    # Not needed anymore
    stdvs <- NULL
    verbose && exit(verbose)
  }
  # Not needed anymore
  medianSE <- units <- NULL
  names(stats) <- getNames(this)[arrays]
  verbose && exit(verbose)

  # Merge boxplot stats?
  if (merge)
    stats <- mergeBoxplotStats(stats)

  attr(stats, "type") <- "NUSE"

  stats
}, protected=TRUE) # calculateNuseStats()