Nothing
R/RmaPlm.R
In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets
###########################################################################/**
# @RdocClass RmaPlm
#
# @title "The RmaPlm class"
#
# \description{
# @classhierarchy
#
# This class represents the log-additive model part of the Robust Multichip
# Analysis (RMA) method described in Irizarry et al (2003).
# }
#
# @synopsis
#
# \arguments{
# \item{...}{Arguments passed to @see "ProbeLevelModel".}
# \item{flavor}{A @character string specifying what model fitting algorithm
# to be used. This makes it possible to get identical estimates as other
# packages.}
# }
#
# \section{Fields and Methods}{
# @allmethods "public"
# }
#
# \section{Model}{
# For a single unit group, the log-additive model of RMA is:
#
# \deqn{log_2(y_{ik}) = \beta_i + \alpha_k + \varepsilon_{ik}}
#
# where \eqn{\beta_i} are the chip effects for arrays \eqn{i=1,...,I},
# and \eqn{\alpha_k} are the probe affinities for probes \eqn{k=1,...,K}.
# The \eqn{\varepsilon_{ik}} are zero-mean noise with equal variance.
# The model is constrained such that \eqn{\sum_k{\alpha_k} = 0}.
#
# Note that all PLM classes must return parameters on the intensity scale.
# For this class that means that \eqn{\theta_i = 2^\beta_i} and
# \eqn{\phi_k = 2^\alpha_k} are returned.
# }
#
# \section{Different flavors of model fitting}{
# There are a few differ algorithms available for fitting the same
# probe-level model. The default and recommended method
# (\code{flavor="affyPLM"}) uses the implementation in the
# \pkg{preprocessCore} package which fits the model parameters robustly
# using an M-estimator (the method used to be in \pkg{affyPLM}).
#
# Alternatively, other model-fitting algorithms are available.
# The algorithm (\code{flavor="oligo"}) used by the \pkg{oligo} package,
# which originates from the \pkg{affy} packages, fits the model using
# median polish, which is a non-robust estimator. Note that this algorithm
# does not constraint the probe-effect parameters to multiply to one on
# the intensity scale. Since the internal function does not return these
# estimates, we can neither rescale them.
# }
#
# @author "HB, KS"
#
# \references{
# Irizarry et al. \emph{Summaries of Affymetrix GeneChip probe level data}.
# NAR, 2003, 31, e15.\cr
# }
#*/###########################################################################
setConstructorS3("RmaPlm", function(..., flavor=c("affyPLM", "oligo")) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Argument 'flavor':
flavor <- match.arg(flavor)
this <- extend(ProbeLevelModel(...), "RmaPlm",
.flavor = flavor,
treatNAsAs = "weights"
)
validate(this)
this
})
setMethodS3("getAsteriskTags", "RmaPlm", function(this, collapse=NULL, ...) {
# Returns 'PLM[,<shift>]'
tags <- NextMethod("getAsteriskTags", collapse=NULL)
tags[1] <- "RMA"
# Add class specific parameter tags
if (this$.flavor != "affyPLM")
tags <- c(tags, this$.flavor)
# Collapse
tags <- paste(tags, collapse=collapse)
tags
}, protected=TRUE)
setMethodS3("getParameters", "RmaPlm", function(this, ...) {
params <- NextMethod("getParameters")
params$flavor <- this$.flavor
params$treatNAsAs <- this$treatNAsAs
params
}, protected=TRUE)
setMethodS3("getProbeAffinityFile", "RmaPlm", function(this, ...) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Get the probe affinities (and create files etc)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
paf <- NextMethod("getProbeAffinityFile")
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Update the encode and decode functions
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
setEncodeFunction(paf, function(groupData, ...) {
phi <- .subset2(groupData, "phi")
stdvs <- .subset2(groupData, "sdPhi")
outliers <- .subset2(groupData, "phiOutliers")
# Encode outliers as the sign of 'pixels'; -1 = TRUE, +1 = FALSE
pixels <- sign(0.5 - as.integer(outliers))
list(intensities=phi, stdvs=stdvs, pixels=pixels)
})
setEncodeFunction(paf, function(groupData, ...) {
list(
intensities = .subset2(groupData, "phi"),
stdvs = .subset2(groupData, "sdPhi"),
# Encode outliers as the sign of 'pixels'; -1 = TRUE, +1 = FALSE
pixels = ifelse(.subset2(groupData, "phiOutliers"), -1, +1)
)
})
## setEncodeFunction(paf, function(groupData, ...) {
## groupData[[3]] <- ifelse(.subset2(groupData, "phiOutliers"), -1, +1)
## names(groupData) <- c("phi", "sdPhi", "pixels")
## groupData
## })
##
## setEncodeFunction(paf, function(groupData, ...) {
## groupData[[3]] <- -1*.subset2(groupData, 3)
## names(groupData) <- c("phi", "sdPhi", "pixels")
## groupData
## })
setDecodeFunction(paf, function(groupData, ...) {
intensities <- .subset2(groupData, "intensities")
stdvs <- .subset2(groupData, "stdvs")
pixels <- .subset2(groupData, "pixels")
# Outliers are encoded by the sign of 'pixels'.
outliers <- as.logical(1-sign(pixels))
list(
phi=intensities,
sdPhi=stdvs,
phiOutliers=outliers
)
})
paf
}, private=TRUE)
setMethodS3("getRlmFitFunctions", "RmaPlm", function(static, withPriors=FALSE, ..., verbose=FALSE) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Argument 'withPriors':
withPriors <- Arguments$getLogical(withPriors)
# Argument 'verbose':
verbose <- Arguments$getVerbose(verbose)
if (verbose) {
pushState(verbose)
on.exit(popState(verbose))
}
fcnList <- NULL
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# First, try the preprocessCore package
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
pkg <- "preprocessCore"
pkgDesc <- packageDescription(pkg)
if (is.list(pkgDesc)) {
ver <- pkgDesc$Version
verbose && cat(verbose, pkg, " version: ", ver)
# Internal sanity check
if (compareVersion(ver, "1.8.0") < 0) {
throw("Requires preprocessCore >= 1.8.0")
}
if (withPriors) {
# To please R CMD check
PACKAGE <- "preprocessCore"
fcnList <- list(
wrlm = function(y, phi, psiCode, psiK, w, scale=NULL) {
# From preprocessCore::rcModelWPLM()
.Call("R_rlm_rma_given_probe_effects",
y, phi, psiCode, psiK, w, scale, PACKAGE=PACKAGE)
},
rlm = function(y, phi, psiCode, psiK, w, scale=NULL) {
# From preprocessCore::rcModelPLM()
.Call("R_rlm_rma_given_probe_effects",
y, phi, psiCode, psiK, scale, PACKAGE=PACKAGE)
}
)
} else {
# To please R CMD check
PACKAGE <- "preprocessCore"
fcnList <- list(
wrlm = function(y, psiCode, psiK, w, scale=NULL) {
# From preprocessCore::rcModelPLM()
.Call("R_wrlm_rma_default_model",
y, psiCode, psiK, w, scale, PACKAGE=PACKAGE)
},
rlm = function(y, psiCode, psiK, w, scale=NULL) {
# From preprocessCore::rcModelPLM()
.Call("R_rlm_rma_default_model",
y, psiCode, psiK, scale, PACKAGE=PACKAGE)
}
)
}
}
if (!is.null(fcnList)) {
.require <- require
.require(pkg, character.only=TRUE) || throw("Package not loaded: ", pkg)
return(fcnList)
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Failure
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
throw("Failed to retrieve RLM fit functions. Please install the 'preprocessCore' package.")
}, static=TRUE, protected=TRUE) # getRlmFitFunctions()
###########################################################################/**
# @RdocMethod getFitUnitGroupFunction
#
# @title "Gets the low-level function that fits the PLM"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{...}{Not used.}
# \item{verbose}{A @logical or @see "R.utils::Verbose".}
# }
#
# \value{
# Returns a @function.
# }
#
# \author{
# Henrik Bengtsson and Ken Simpson (WEHI) utilizing Ben Bolstad's
# \pkg{preprocessCore} package.
# }
#
# \seealso{
# @seeclass
# }
#*/###########################################################################
setMethodS3("getFitUnitGroupFunction", "RmaPlm", function(this, ..., verbose=FALSE) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Argument 'verbose':
verbose <- Arguments$getVerbose(verbose)
if (verbose) {
pushState(verbose)
on.exit(popState(verbose))
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Thresholds for skipping/using median polish
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
skipThreshold <- getOption(aromaSettings,
"models/RmaPlm/skipThreshold", c(Inf, Inf))
medianPolishThreshold <- getOption(aromaSettings,
"models/RmaPlm/medianPolishThreshold", c(Inf, Inf))
flavor <- this$.flavor
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# rmaModelAffyPlm()
# Author: Henrik Bengtsson, UC Berkeley.
# Requires: affyPLM() by Ben Bolstad.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
rmaModelAffyPlm <- function(y, priors=NULL, ..., psiCode=0, psiK=1.345){
# Assert right dimensions of 'y'.
# If input data are dimensionless, return NAs. /KS 2006-01-30
dim <- dim(y)
if (is.null(dim)) {
nbrOfArrays <- length(getDataSet(this))
return(list(theta=rep(NA_real_, times=nbrOfArrays),
sdTheta=rep(NA_real_, times=nbrOfArrays),
thetaOutliers=rep(NA_real_, times=nbrOfArrays),
phi=c(),
sdPhi=c(),
phiOutliers=c()
)
)
}
if (length(dim) != 2) {
str(y)
stop("Argument 'y' must have two dimensions: ",
paste(dim, collapse="x"))
}
K <- dim[1]; # Number of probes
I <- dim[2]; # Number of arrays
# Too many probes?
if (K > skipThreshold[1] && I > skipThreshold[2]) {
warning("Ignoring a unit group when fitting probe-level model, because it has a ridiculously large number of data points: ", paste(dim, collapse="x"), " > ", paste(skipThreshold, collapse="x"))
naValue <- NA_real_
return(list(theta=rep(naValue, times=I),
sdTheta=rep(naValue, times=I),
thetaOutliers=rep(naValue, times=I),
phi=rep(naValue, times=K),
sdPhi=rep(naValue, times=K),
phiOutliers=rep(naValue, times=K)
)
)
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Transform data
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Add shift
y <- y + shift
# Log-additive model
y <- log(y, base=2)
# Look for cells that have NAs in at least one sample?
w <- NULL
nasRemoved <- FALSE
if (treatNAsAs == "ignore") {
hasNAs <- FALSE
} else {
isNA <- is.na(y)
hasNAs <- any(isNA)
if (hasNAs) {
if (treatNAsAs == "weights") {
badCells <- colAlls(isNA)
if (any(badCells)) {
return(list(theta=rep(NA_real_, times=I),
sdTheta=rep(NA_real_, times=I),
thetaOutliers=rep(NA_real_, times=I),
phi=rep(NA_real_, times=K),
sdPhi=rep(NA_real_, times=K),
phiOutliers=rep(NA_real_, times=K)
)
)
}
w <- matrix(1, nrow=K, ncol=I)
w[isNA] <- 0
y[isNA] <- 0
} else if (treatNAsAs == "0") {
y[isNA] <- 0
hasNAs <- FALSE
} else if (treatNAsAs == "NA") {
K0 <- K; # Number of cells
okCells <- !rowAnys(isNA)
# Analyze only valid cells
y <- y[okCells,,drop=FALSE]
nasRemoved <- TRUE
hasNAs <- FALSE
# No valid cells left?
if (nrow(y) == 0) {
return(list(theta=rep(NA_real_, times=I),
sdTheta=rep(NA_real_, times=I),
thetaOutliers=rep(NA_real_, times=I),
phi=rep(NA_real_, times=K0),
sdPhi=rep(NA_real_, times=K0),
phiOutliers=rep(NA_real_, times=K0)
)
)
}
}
} # if (hasNAs)
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Fit model
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
hasPriors <- !is.null(priors)
if (hasPriors) {
paf <- priors$probeAffinities[[1]]
# Sanity check
stopifnot(!is.null(paf))
phi <- paf$phi
# Sanity check
stopifnot(!is.null(phi))
# Sanity check
stopifnot(length(phi) == K)
sdPhi <- paf$sdPhi
# Log-additive model
alpha <- log(phi, base=2)
if (!is.null(w)) {
fit <- wrlm(y, alpha, psiCode, psiK, w)
} else {
fit <- rlm(y, alpha, psiCode, psiK)
}
} else {
# Use median polish for large probesets (that doesn't have NAs)?
if (K > medianPolishThreshold[1] && I > medianPolishThreshold[2] && !hasNAs) {
mp <- medpolish(y, trace.iter=FALSE)
fit <- list(
Estimates = c(mp$overall+mp$col, mp$row),
StdErrors = rep(0, length(c(mp$row, mp$col)))
)
} else {
# Fit model using preprocessCore/affyPLM code
if (!is.null(w)) {
fit <- wrlm(y, psiCode, psiK, w)
} else {
fit <- rlm(y, psiCode, psiK)
}
}
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Extract parameters
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
est <- fit$Estimates
se <- fit$StdErrors
# Chip effects
beta <- est[1:I]
# On the intensity scale
theta <- 2^beta
# Probe affinities
if (!hasPriors) {
alpha <- est[(I+1):length(est)]
alpha[length(alpha)] <- -sum(alpha[1:(length(alpha)-1)])
# On the intensity scale
phi <- 2^alpha
}
# The RMA model is fitted with constraint sum(alpha) = 0, that is,
# such that prod(phi) = 1.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# A fit function must return: theta, sdTheta, thetaOutliers,
# phi, sdPhi, phiOutliers.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (is.null(se)) {
# For affyPLM v1.10.0 (2006-09-26) or older.
sdTheta <- rep(1, times=I)
if (!hasPriors) {
sdPhi <- rep(1, times=K)
}
} else {
# For affyPLM v1.11.6 (2006-11-01) or newer.
sdTheta <- 2^(se[1:I])
if (!hasPriors) {
sdPhi <- 2^(se[(I+1):length(se)])
}
}
# Handle NAs?
if (nasRemoved) {
if (treatNAsAs == "NA") {
naValue <- NA_real_
phi0 <- rep(naValue, times=K0)
phi0[okCells] <- phi
phi <- phi0
sdPhi0 <- rep(naValue, times=K0)
sdPhi0[okCells] <- sdPhi
sdPhi <- sdPhi0
K <- K0
}
}
thetaOutliers <- rep(FALSE, times=I)
phiOutliers <- rep(FALSE, times=K)
# Return data on the intensity scale
list(theta=theta, sdTheta=sdTheta, thetaOutliers=thetaOutliers,
phi=phi, sdPhi=sdPhi, phiOutliers=phiOutliers)
} # rmaModelAffyPlm()
attr(rmaModelAffyPlm, "name") <- "rmaModelAffyPlm"
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# rmaModelOligo().
# Author: Henrik Bengtsson, WEHI, 2006-12-11.
# Requires: oligo() by Benilto Carvalho et al.
# Why: To fully imitate CRLMM in oligo.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (flavor == "oligo") {
# First, try to see if package is available
pkg <- "oligo"
.require <- require
.require(pkg, character.only=TRUE) || throw("Package not loaded: ", pkg)
pkgDesc <- packageDescription(pkg)
ver <- pkgDesc$Version
verbose && cat(verbose, pkg, " version: ", ver)
if (compareVersion(ver, "1.7.19") >= 0) {
# HB 2009-05-09:
# The API of the native function rma_c_complete_copy()
# has been updated yet again, but the good thing,
# there is now a basicRMA() wrapper function.
# Lookup oligo::basicRMA() once; '::' is expensive
oligo_basicRMA <- oligo::basicRMA
fitRma <- function(y, unitNames, nbrOfUnits, ...) {
oligo_basicRMA(y, pnVec=unitNames, background=FALSE,
normalize=FALSE, verbose=FALSE)
} # fitRma()
} else {
throw("Non-supported version (< 1.7.19) of 'oligo' detected. Please update the 'oligo' package: ", ver)
}
}
rmaModelOligo <- function(y, priors=NULL, ...) {
if (!is.null(priors)) {
throw("NOT IMPLEMENTED: Internal rmaModelOligo() does not support prior parameters.")
}
# Add shift
y <- y + shift
# Assert right dimensions of 'y'.
dim <- dim(y)
if (length(dim) != 2) {
str(y)
stop("Argument 'y' must have two dimensions: ",
paste(dim, collapse="x"))
}
K <- dim[1]; # Number of probes
I <- dim[2]; # Number of arrays
# Too many probes?
if (K > skipThreshold[1] && I > skipThreshold[2]) {
warning("Ignoring a unit group when fitting probe-level model, because it has a ridiculously large number of data points: ", paste(dim, collapse="x"), " > ", paste(skipThreshold, collapse="x"))
return(list(theta=rep(NA_real_, times=I),
sdTheta=rep(NA_real_, times=I),
thetaOutliers=rep(NA_real_, times=I),
phi=rep(NA_real_, times=K),
sdPhi=rep(NA_real_, times=K),
phiOutliers=rep(NA_real_, times=K)
)
)
}
# make factor variables for chip and probe
unitNames <- rep("X", K); # dummy probe names
nbrOfUnits <- as.integer(1); # Only one unit group is fitted
# Each call to fitRma() outputs "Calculating Expression".
fit <- fitRma(y, unitNames, nbrOfUnits)
# Extract probe affinities and chip estimates
est <- fit[1,,drop=TRUE]; # Only one unit
# Chip effects
beta <- est[1:I]
# Probe affinities
alpha <- rep(0, K); # Not returned by fitRma()!
# Estimates on the intensity scale
theta <- 2^beta
phi <- 2^alpha
# The RMA model is fitted with constraint sum(alpha) = 0, that is,
# such that prod(phi) = 1.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# A fit function must return: theta, sdTheta, thetaOutliers,
# phi, sdPhi, phiOutliers.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
sdTheta <- rep(1, I)
thetaOutliers <- rep(FALSE, I)
sdPhi <- rep(1, K)
phiOutliers <- rep(FALSE, K)
# Return data on the intensity scale
list(theta=theta, sdTheta=sdTheta, thetaOutliers=thetaOutliers,
phi=phi, sdPhi=sdPhi, phiOutliers=phiOutliers)
} # rmaModelOligo()
attr(rmaModelOligo, "name") <- "rmaModelOligo"
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Main
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
verbose && enter(verbose, "Getting the PLM fit function")
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Get the flavor of fitting algorithm for the RMA PLM
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
verbose && enter(verbose, "Selecting fit function depending on 'flavor'")
verbose && cat(verbose, "Flavor: ", flavor)
priors <- getListOfPriors(this)
hasPriors <- !is.null(priors)
verbose && cat(verbose, "Has priors: ", hasPriors)
if (hasPriors) {
# Sanity check
stopifnot(is.element("probeAffinities", names(priors)))
}
# Shift signals?
shift <- this$shift
if (is.null(shift))
shift <- 0
verbose && cat(verbose, "Amount of shift: ", shift)
# Handle non-positive signals?
treatNAsAs <- this$treatNAsAs
if (is.null(treatNAsAs))
treatNAsAs <- "ignore"
verbose && cat(verbose, "treatNAsAs: ", treatNAsAs)
if (flavor == "affyPLM") {
fcnList <- RmaPlm$getRlmFitFunctions(withPriors=hasPriors, verbose=less(verbose))
verbose && str(verbose, fcnList)
# To please R CMD check
rlm <- wrlm <- NULL; rm(list=c("rlm", "wrlm"))
attachLocally(fcnList)
rmaModel <- rmaModelAffyPlm
} else if (flavor == "oligo") {
requireNamespace("oligo") || throw("Package not loaded: oligo")
rmaModel <- rmaModelOligo
} else {
throw("Cannot get fit function for RMA PLM. Unknown flavor: ", flavor)
}
verbose && str(verbose, rmaModel)
verbose && exit(verbose)
# Test that it works and is available.
verbose && enter(verbose, "Validating the fit function on some dummy data")
ok <- FALSE
tryCatch({
y <- matrix(1:12+0.1, ncol=3)
if (hasPriors) {
verbose && cat(verbose, "With prior probe affinities")
phi <- c(0.7630639, 0.9068485, 1.1208795, 1.2892744)
sdPhi <- c(1.101706, 1.091220, 1.091220, 1.094554)
priors <- list(probeAffinities=list("foo"=list(phi=phi, sdPhi=sdPhi)))
res <- rmaModel(y, priors=priors)
} else {
res <- rmaModel(y)
}
ok <- TRUE
}, error = function(ex) {
print(ex)
})
if (!ok) {
throw("The fit function for requested RMA PLM flavor failed: ", flavor)
}
verbose && exit(verbose)
verbose && exit(verbose)
rmaModel
}, private=TRUE) # getFitUnitGroupFunction()
setMethodS3("getCalculateResidualsFunction", "RmaPlm", function(static, ...) {
function(y, yhat) {
y/yhat
}
}, static=TRUE, protected=TRUE)
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###########################################################################/**
# @RdocClass RmaPlm
#
# @title "The RmaPlm class"
#
# \description{
# @classhierarchy
#
# This class represents the log-additive model part of the Robust Multichip
# Analysis (RMA) method described in Irizarry et al (2003).
# }
#
# @synopsis
#
# \arguments{
# \item{...}{Arguments passed to @see "ProbeLevelModel".}
# \item{flavor}{A @character string specifying what model fitting algorithm
# to be used. This makes it possible to get identical estimates as other
# packages.}
# }
#
# \section{Fields and Methods}{
# @allmethods "public"
# }
#
# \section{Model}{
# For a single unit group, the log-additive model of RMA is:
#
# \deqn{log_2(y_{ik}) = \beta_i + \alpha_k + \varepsilon_{ik}}
#
# where \eqn{\beta_i} are the chip effects for arrays \eqn{i=1,...,I},
# and \eqn{\alpha_k} are the probe affinities for probes \eqn{k=1,...,K}.
# The \eqn{\varepsilon_{ik}} are zero-mean noise with equal variance.
# The model is constrained such that \eqn{\sum_k{\alpha_k} = 0}.
#
# Note that all PLM classes must return parameters on the intensity scale.
# For this class that means that \eqn{\theta_i = 2^\beta_i} and
# \eqn{\phi_k = 2^\alpha_k} are returned.
# }
#
# \section{Different flavors of model fitting}{
# There are a few differ algorithms available for fitting the same
# probe-level model. The default and recommended method
# (\code{flavor="affyPLM"}) uses the implementation in the
# \pkg{preprocessCore} package which fits the model parameters robustly
# using an M-estimator (the method used to be in \pkg{affyPLM}).
#
# Alternatively, other model-fitting algorithms are available.
# The algorithm (\code{flavor="oligo"}) used by the \pkg{oligo} package,
# which originates from the \pkg{affy} packages, fits the model using
# median polish, which is a non-robust estimator. Note that this algorithm
# does not constraint the probe-effect parameters to multiply to one on
# the intensity scale. Since the internal function does not return these
# estimates, we can neither rescale them.
# }
#
# @author "HB, KS"
#
# \references{
# Irizarry et al. \emph{Summaries of Affymetrix GeneChip probe level data}.
# NAR, 2003, 31, e15.\cr
# }
#*/###########################################################################
setConstructorS3("RmaPlm", function(..., flavor=c("affyPLM", "oligo")) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Argument 'flavor':
flavor <- match.arg(flavor)
this <- extend(ProbeLevelModel(...), "RmaPlm",
.flavor = flavor,
treatNAsAs = "weights"
)
validate(this)
this
})
setMethodS3("getAsteriskTags", "RmaPlm", function(this, collapse=NULL, ...) {
# Returns 'PLM[,<shift>]'
tags <- NextMethod("getAsteriskTags", collapse=NULL)
tags[1] <- "RMA"
# Add class specific parameter tags
if (this$.flavor != "affyPLM")
tags <- c(tags, this$.flavor)
# Collapse
tags <- paste(tags, collapse=collapse)
tags
}, protected=TRUE)
setMethodS3("getParameters", "RmaPlm", function(this, ...) {
params <- NextMethod("getParameters")
params$flavor <- this$.flavor
params$treatNAsAs <- this$treatNAsAs
params
}, protected=TRUE)
setMethodS3("getProbeAffinityFile", "RmaPlm", function(this, ...) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Get the probe affinities (and create files etc)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
paf <- NextMethod("getProbeAffinityFile")
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Update the encode and decode functions
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
setEncodeFunction(paf, function(groupData, ...) {
phi <- .subset2(groupData, "phi")
stdvs <- .subset2(groupData, "sdPhi")
outliers <- .subset2(groupData, "phiOutliers")
# Encode outliers as the sign of 'pixels'; -1 = TRUE, +1 = FALSE
pixels <- sign(0.5 - as.integer(outliers))
list(intensities=phi, stdvs=stdvs, pixels=pixels)
})
setEncodeFunction(paf, function(groupData, ...) {
list(
intensities = .subset2(groupData, "phi"),
stdvs = .subset2(groupData, "sdPhi"),
# Encode outliers as the sign of 'pixels'; -1 = TRUE, +1 = FALSE
pixels = ifelse(.subset2(groupData, "phiOutliers"), -1, +1)
)
})
## setEncodeFunction(paf, function(groupData, ...) {
## groupData[[3]] <- ifelse(.subset2(groupData, "phiOutliers"), -1, +1)
## names(groupData) <- c("phi", "sdPhi", "pixels")
## groupData
## })
##
## setEncodeFunction(paf, function(groupData, ...) {
## groupData[[3]] <- -1*.subset2(groupData, 3)
## names(groupData) <- c("phi", "sdPhi", "pixels")
## groupData
## })
setDecodeFunction(paf, function(groupData, ...) {
intensities <- .subset2(groupData, "intensities")
stdvs <- .subset2(groupData, "stdvs")
pixels <- .subset2(groupData, "pixels")
# Outliers are encoded by the sign of 'pixels'.
outliers <- as.logical(1-sign(pixels))
list(
phi=intensities,
sdPhi=stdvs,
phiOutliers=outliers
)
})
paf
}, private=TRUE)
setMethodS3("getRlmFitFunctions", "RmaPlm", function(static, withPriors=FALSE, ..., verbose=FALSE) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Argument 'withPriors':
withPriors <- Arguments$getLogical(withPriors)
# Argument 'verbose':
verbose <- Arguments$getVerbose(verbose)
if (verbose) {
pushState(verbose)
on.exit(popState(verbose))
}
fcnList <- NULL
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# First, try the preprocessCore package
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
pkg <- "preprocessCore"
pkgDesc <- packageDescription(pkg)
if (is.list(pkgDesc)) {
ver <- pkgDesc$Version
verbose && cat(verbose, pkg, " version: ", ver)
# Internal sanity check
if (compareVersion(ver, "1.8.0") < 0) {
throw("Requires preprocessCore >= 1.8.0")
}
if (withPriors) {
# To please R CMD check
PACKAGE <- "preprocessCore"
fcnList <- list(
wrlm = function(y, phi, psiCode, psiK, w, scale=NULL) {
# From preprocessCore::rcModelWPLM()
.Call("R_rlm_rma_given_probe_effects",
y, phi, psiCode, psiK, w, scale, PACKAGE=PACKAGE)
},
rlm = function(y, phi, psiCode, psiK, w, scale=NULL) {
# From preprocessCore::rcModelPLM()
.Call("R_rlm_rma_given_probe_effects",
y, phi, psiCode, psiK, scale, PACKAGE=PACKAGE)
}
)
} else {
# To please R CMD check
PACKAGE <- "preprocessCore"
fcnList <- list(
wrlm = function(y, psiCode, psiK, w, scale=NULL) {
# From preprocessCore::rcModelPLM()
.Call("R_wrlm_rma_default_model",
y, psiCode, psiK, w, scale, PACKAGE=PACKAGE)
},
rlm = function(y, psiCode, psiK, w, scale=NULL) {
# From preprocessCore::rcModelPLM()
.Call("R_rlm_rma_default_model",
y, psiCode, psiK, scale, PACKAGE=PACKAGE)
}
)
}
}
if (!is.null(fcnList)) {
.require <- require
.require(pkg, character.only=TRUE) || throw("Package not loaded: ", pkg)
return(fcnList)
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Failure
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
throw("Failed to retrieve RLM fit functions. Please install the 'preprocessCore' package.")
}, static=TRUE, protected=TRUE) # getRlmFitFunctions()
###########################################################################/**
# @RdocMethod getFitUnitGroupFunction
#
# @title "Gets the low-level function that fits the PLM"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{...}{Not used.}
# \item{verbose}{A @logical or @see "R.utils::Verbose".}
# }
#
# \value{
# Returns a @function.
# }
#
# \author{
# Henrik Bengtsson and Ken Simpson (WEHI) utilizing Ben Bolstad's
# \pkg{preprocessCore} package.
# }
#
# \seealso{
# @seeclass
# }
#*/###########################################################################
setMethodS3("getFitUnitGroupFunction", "RmaPlm", function(this, ..., verbose=FALSE) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Argument 'verbose':
verbose <- Arguments$getVerbose(verbose)
if (verbose) {
pushState(verbose)
on.exit(popState(verbose))
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Thresholds for skipping/using median polish
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
skipThreshold <- getOption(aromaSettings,
"models/RmaPlm/skipThreshold", c(Inf, Inf))
medianPolishThreshold <- getOption(aromaSettings,
"models/RmaPlm/medianPolishThreshold", c(Inf, Inf))
flavor <- this$.flavor
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# rmaModelAffyPlm()
# Author: Henrik Bengtsson, UC Berkeley.
# Requires: affyPLM() by Ben Bolstad.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
rmaModelAffyPlm <- function(y, priors=NULL, ..., psiCode=0, psiK=1.345){
# Assert right dimensions of 'y'.
# If input data are dimensionless, return NAs. /KS 2006-01-30
dim <- dim(y)
if (is.null(dim)) {
nbrOfArrays <- length(getDataSet(this))
return(list(theta=rep(NA_real_, times=nbrOfArrays),
sdTheta=rep(NA_real_, times=nbrOfArrays),
thetaOutliers=rep(NA_real_, times=nbrOfArrays),
phi=c(),
sdPhi=c(),
phiOutliers=c()
)
)
}
if (length(dim) != 2) {
str(y)
stop("Argument 'y' must have two dimensions: ",
paste(dim, collapse="x"))
}
K <- dim[1]; # Number of probes
I <- dim[2]; # Number of arrays
# Too many probes?
if (K > skipThreshold[1] && I > skipThreshold[2]) {
warning("Ignoring a unit group when fitting probe-level model, because it has a ridiculously large number of data points: ", paste(dim, collapse="x"), " > ", paste(skipThreshold, collapse="x"))
naValue <- NA_real_
return(list(theta=rep(naValue, times=I),
sdTheta=rep(naValue, times=I),
thetaOutliers=rep(naValue, times=I),
phi=rep(naValue, times=K),
sdPhi=rep(naValue, times=K),
phiOutliers=rep(naValue, times=K)
)
)
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Transform data
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Add shift
y <- y + shift
# Log-additive model
y <- log(y, base=2)
# Look for cells that have NAs in at least one sample?
w <- NULL
nasRemoved <- FALSE
if (treatNAsAs == "ignore") {
hasNAs <- FALSE
} else {
isNA <- is.na(y)
hasNAs <- any(isNA)
if (hasNAs) {
if (treatNAsAs == "weights") {
badCells <- colAlls(isNA)
if (any(badCells)) {
return(list(theta=rep(NA_real_, times=I),
sdTheta=rep(NA_real_, times=I),
thetaOutliers=rep(NA_real_, times=I),
phi=rep(NA_real_, times=K),
sdPhi=rep(NA_real_, times=K),
phiOutliers=rep(NA_real_, times=K)
)
)
}
w <- matrix(1, nrow=K, ncol=I)
w[isNA] <- 0
y[isNA] <- 0
} else if (treatNAsAs == "0") {
y[isNA] <- 0
hasNAs <- FALSE
} else if (treatNAsAs == "NA") {
K0 <- K; # Number of cells
okCells <- !rowAnys(isNA)
# Analyze only valid cells
y <- y[okCells,,drop=FALSE]
nasRemoved <- TRUE
hasNAs <- FALSE
# No valid cells left?
if (nrow(y) == 0) {
return(list(theta=rep(NA_real_, times=I),
sdTheta=rep(NA_real_, times=I),
thetaOutliers=rep(NA_real_, times=I),
phi=rep(NA_real_, times=K0),
sdPhi=rep(NA_real_, times=K0),
phiOutliers=rep(NA_real_, times=K0)
)
)
}
}
} # if (hasNAs)
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Fit model
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
hasPriors <- !is.null(priors)
if (hasPriors) {
paf <- priors$probeAffinities[[1]]
# Sanity check
stopifnot(!is.null(paf))
phi <- paf$phi
# Sanity check
stopifnot(!is.null(phi))
# Sanity check
stopifnot(length(phi) == K)
sdPhi <- paf$sdPhi
# Log-additive model
alpha <- log(phi, base=2)
if (!is.null(w)) {
fit <- wrlm(y, alpha, psiCode, psiK, w)
} else {
fit <- rlm(y, alpha, psiCode, psiK)
}
} else {
# Use median polish for large probesets (that doesn't have NAs)?
if (K > medianPolishThreshold[1] && I > medianPolishThreshold[2] && !hasNAs) {
mp <- medpolish(y, trace.iter=FALSE)
fit <- list(
Estimates = c(mp$overall+mp$col, mp$row),
StdErrors = rep(0, length(c(mp$row, mp$col)))
)
} else {
# Fit model using preprocessCore/affyPLM code
if (!is.null(w)) {
fit <- wrlm(y, psiCode, psiK, w)
} else {
fit <- rlm(y, psiCode, psiK)
}
}
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Extract parameters
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
est <- fit$Estimates
se <- fit$StdErrors
# Chip effects
beta <- est[1:I]
# On the intensity scale
theta <- 2^beta
# Probe affinities
if (!hasPriors) {
alpha <- est[(I+1):length(est)]
alpha[length(alpha)] <- -sum(alpha[1:(length(alpha)-1)])
# On the intensity scale
phi <- 2^alpha
}
# The RMA model is fitted with constraint sum(alpha) = 0, that is,
# such that prod(phi) = 1.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# A fit function must return: theta, sdTheta, thetaOutliers,
# phi, sdPhi, phiOutliers.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (is.null(se)) {
# For affyPLM v1.10.0 (2006-09-26) or older.
sdTheta <- rep(1, times=I)
if (!hasPriors) {
sdPhi <- rep(1, times=K)
}
} else {
# For affyPLM v1.11.6 (2006-11-01) or newer.
sdTheta <- 2^(se[1:I])
if (!hasPriors) {
sdPhi <- 2^(se[(I+1):length(se)])
}
}
# Handle NAs?
if (nasRemoved) {
if (treatNAsAs == "NA") {
naValue <- NA_real_
phi0 <- rep(naValue, times=K0)
phi0[okCells] <- phi
phi <- phi0
sdPhi0 <- rep(naValue, times=K0)
sdPhi0[okCells] <- sdPhi
sdPhi <- sdPhi0
K <- K0
}
}
thetaOutliers <- rep(FALSE, times=I)
phiOutliers <- rep(FALSE, times=K)
# Return data on the intensity scale
list(theta=theta, sdTheta=sdTheta, thetaOutliers=thetaOutliers,
phi=phi, sdPhi=sdPhi, phiOutliers=phiOutliers)
} # rmaModelAffyPlm()
attr(rmaModelAffyPlm, "name") <- "rmaModelAffyPlm"
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# rmaModelOligo().
# Author: Henrik Bengtsson, WEHI, 2006-12-11.
# Requires: oligo() by Benilto Carvalho et al.
# Why: To fully imitate CRLMM in oligo.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (flavor == "oligo") {
# First, try to see if package is available
pkg <- "oligo"
.require <- require
.require(pkg, character.only=TRUE) || throw("Package not loaded: ", pkg)
pkgDesc <- packageDescription(pkg)
ver <- pkgDesc$Version
verbose && cat(verbose, pkg, " version: ", ver)
if (compareVersion(ver, "1.7.19") >= 0) {
# HB 2009-05-09:
# The API of the native function rma_c_complete_copy()
# has been updated yet again, but the good thing,
# there is now a basicRMA() wrapper function.
# Lookup oligo::basicRMA() once; '::' is expensive
oligo_basicRMA <- oligo::basicRMA
fitRma <- function(y, unitNames, nbrOfUnits, ...) {
oligo_basicRMA(y, pnVec=unitNames, background=FALSE,
normalize=FALSE, verbose=FALSE)
} # fitRma()
} else {
throw("Non-supported version (< 1.7.19) of 'oligo' detected. Please update the 'oligo' package: ", ver)
}
}
rmaModelOligo <- function(y, priors=NULL, ...) {
if (!is.null(priors)) {
throw("NOT IMPLEMENTED: Internal rmaModelOligo() does not support prior parameters.")
}
# Add shift
y <- y + shift
# Assert right dimensions of 'y'.
dim <- dim(y)
if (length(dim) != 2) {
str(y)
stop("Argument 'y' must have two dimensions: ",
paste(dim, collapse="x"))
}
K <- dim[1]; # Number of probes
I <- dim[2]; # Number of arrays
# Too many probes?
if (K > skipThreshold[1] && I > skipThreshold[2]) {
warning("Ignoring a unit group when fitting probe-level model, because it has a ridiculously large number of data points: ", paste(dim, collapse="x"), " > ", paste(skipThreshold, collapse="x"))
return(list(theta=rep(NA_real_, times=I),
sdTheta=rep(NA_real_, times=I),
thetaOutliers=rep(NA_real_, times=I),
phi=rep(NA_real_, times=K),
sdPhi=rep(NA_real_, times=K),
phiOutliers=rep(NA_real_, times=K)
)
)
}
# make factor variables for chip and probe
unitNames <- rep("X", K); # dummy probe names
nbrOfUnits <- as.integer(1); # Only one unit group is fitted
# Each call to fitRma() outputs "Calculating Expression".
fit <- fitRma(y, unitNames, nbrOfUnits)
# Extract probe affinities and chip estimates
est <- fit[1,,drop=TRUE]; # Only one unit
# Chip effects
beta <- est[1:I]
# Probe affinities
alpha <- rep(0, K); # Not returned by fitRma()!
# Estimates on the intensity scale
theta <- 2^beta
phi <- 2^alpha
# The RMA model is fitted with constraint sum(alpha) = 0, that is,
# such that prod(phi) = 1.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# A fit function must return: theta, sdTheta, thetaOutliers,
# phi, sdPhi, phiOutliers.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
sdTheta <- rep(1, I)
thetaOutliers <- rep(FALSE, I)
sdPhi <- rep(1, K)
phiOutliers <- rep(FALSE, K)
# Return data on the intensity scale
list(theta=theta, sdTheta=sdTheta, thetaOutliers=thetaOutliers,
phi=phi, sdPhi=sdPhi, phiOutliers=phiOutliers)
} # rmaModelOligo()
attr(rmaModelOligo, "name") <- "rmaModelOligo"
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Main
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
verbose && enter(verbose, "Getting the PLM fit function")
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Get the flavor of fitting algorithm for the RMA PLM
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
verbose && enter(verbose, "Selecting fit function depending on 'flavor'")
verbose && cat(verbose, "Flavor: ", flavor)
priors <- getListOfPriors(this)
hasPriors <- !is.null(priors)
verbose && cat(verbose, "Has priors: ", hasPriors)
if (hasPriors) {
# Sanity check
stopifnot(is.element("probeAffinities", names(priors)))
}
# Shift signals?
shift <- this$shift
if (is.null(shift))
shift <- 0
verbose && cat(verbose, "Amount of shift: ", shift)
# Handle non-positive signals?
treatNAsAs <- this$treatNAsAs
if (is.null(treatNAsAs))
treatNAsAs <- "ignore"
verbose && cat(verbose, "treatNAsAs: ", treatNAsAs)
if (flavor == "affyPLM") {
fcnList <- RmaPlm$getRlmFitFunctions(withPriors=hasPriors, verbose=less(verbose))
verbose && str(verbose, fcnList)
# To please R CMD check
rlm <- wrlm <- NULL; rm(list=c("rlm", "wrlm"))
attachLocally(fcnList)
rmaModel <- rmaModelAffyPlm
} else if (flavor == "oligo") {
requireNamespace("oligo") || throw("Package not loaded: oligo")
rmaModel <- rmaModelOligo
} else {
throw("Cannot get fit function for RMA PLM. Unknown flavor: ", flavor)
}
verbose && str(verbose, rmaModel)
verbose && exit(verbose)
# Test that it works and is available.
verbose && enter(verbose, "Validating the fit function on some dummy data")
ok <- FALSE
tryCatch({
y <- matrix(1:12+0.1, ncol=3)
if (hasPriors) {
verbose && cat(verbose, "With prior probe affinities")
phi <- c(0.7630639, 0.9068485, 1.1208795, 1.2892744)
sdPhi <- c(1.101706, 1.091220, 1.091220, 1.094554)
priors <- list(probeAffinities=list("foo"=list(phi=phi, sdPhi=sdPhi)))
res <- rmaModel(y, priors=priors)
} else {
res <- rmaModel(y)
}
ok <- TRUE
}, error = function(ex) {
print(ex)
})
if (!ok) {
throw("The fit function for requested RMA PLM flavor failed: ", flavor)
}
verbose && exit(verbose)
verbose && exit(verbose)
rmaModel
}, private=TRUE) # getFitUnitGroupFunction()
setMethodS3("getCalculateResidualsFunction", "RmaPlm", function(static, ...) {
function(y, yhat) {
y/yhat
}
}, static=TRUE, protected=TRUE)
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