[Robast-commits] r464 - in pkg/RobLoxBioC: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Mar 3 23:30:53 CET 2012
Author: stamats
Date: 2012-03-03 23:30:52 +0100 (Sat, 03 Mar 2012)
New Revision: 464
Added:
pkg/RobLoxBioC/R/robloxbiocBeadLevelData.R
Removed:
pkg/RobLoxBioC/R/robloxbiocBeadLevelList.R
Modified:
pkg/RobLoxBioC/DESCRIPTION
pkg/RobLoxBioC/man/robloxbioc.Rd
Log:
forgot to add signature from BeadLevelList to BeadLevelData
Modified: pkg/RobLoxBioC/DESCRIPTION
===================================================================
--- pkg/RobLoxBioC/DESCRIPTION 2012-03-03 22:18:35 UTC (rev 463)
+++ pkg/RobLoxBioC/DESCRIPTION 2012-03-03 22:30:52 UTC (rev 464)
@@ -5,7 +5,6 @@
Description: Functions for the determination of optimally robust influence curves and
estimators for preprocessing omics data, in particular gene expression data.
Depends: R(>= 2.14.0), methods, Biobase, affy, beadarray, distr, RobLox, lattice, RColorBrewer
-Suggests: beadarrayExampleData
Author: Matthias Kohl <Matthias.Kohl at stamats.de>
Maintainer: Matthias Kohl <Matthias.Kohl at stamats.de>
LazyLoad: yes
Copied: pkg/RobLoxBioC/R/robloxbiocBeadLevelData.R (from rev 462, pkg/RobLoxBioC/R/robloxbiocBeadLevelList.R)
===================================================================
--- pkg/RobLoxBioC/R/robloxbiocBeadLevelData.R (rev 0)
+++ pkg/RobLoxBioC/R/robloxbiocBeadLevelData.R 2012-03-03 22:30:52 UTC (rev 464)
@@ -0,0 +1,202 @@
+setMethod("robloxbioc", signature(x = "BeadLevelData"),
+ function(x, log = TRUE, imagesPerArray = 1, what = "G", probes = NULL, arrays = NULL,
+ eps = NULL, eps.lower = 0, eps.upper = 0.05, steps = 3L,
+ fsCor = TRUE, mad0 = 1e-4){
+ BLData <- x
+ arraynms <- sectionNames(BLData)
+ if(!is.null(arrays) && !is.character(arrays)) arraynms <- arraynms[arrays]
+ if(is.character(arrays)) arraynms <- which(arraynms %in% arrays)
+ len <- length(arraynms)
+ what <- match.arg(what, c("G", "R", "RG", "M", "A", "beta"))
+ whatelse <- ""
+ if(what == "RG"){
+ if(BLData at arrayInfo$channels == "two"){
+ what <- "G"
+ whatelse <- "R"
+ }else{
+ stop("Need two-channel data to calculate summary R and G values")
+ }
+ }
+ if(imagesPerArray == 1){
+ pr <- getBeadData(BLData, what = "ProbeID", array = arraynms[1])
+ sel <- pr != 0
+ pr <- pr[sel]
+ finten <- getBeadData(BLData, what = what, array = arraynms[1])[sel]
+ if(log) finten <- log2(finten)
+ nasinf <- !is.finite(finten) | is.na(finten)
+ finten <- finten[!nasinf]
+ }
+ else if(imagesPerArray == 2){
+ if(length(arraynms)%%2 != 0)
+ stop("Need an even number of arrays when 'imagesPerArray=2'")
+ arrayord <- order(arraynms)
+ arraynms <- arraynms[arrayord]
+ tmp <- unlist(strsplit(arraynms, "_"))
+ chipnums <- tmp[seq(1, length(tmp), by = 3)]
+ pos <- tmp[seq(2, length(tmp), by = 3)]
+ stripnum <- as.numeric(tmp[seq(3, length(tmp), by = 3)])
+ check <- ((chipnums[seq(1, len, by = 2)] == chipnums[seq(2, len, by = 2)])
+ & (pos[seq(1, len, by = 2)] == pos[seq(2, len, by = 2)])
+ & (stripnum[seq(1, len, by = 2)] == stripnum[seq(2, len, by = 2)] - 1))
+ if (sum(check) != length(check))
+ stop("Missing arrays")
+ sel1 <- getBeadData(BLData, what = "ProbeID", array = arraynms[1]) != 0
+ sel2 <- getBeadData(BLData, what = "ProbeID", array = arraynms[2]) != 0
+ pr <- append(getBeadData(BLData, what = "ProbeID", array = arraynms[1])[sel1],
+ getBeadData(BLData, what = "ProbeID", array = arraynms[2])[sel2])
+ finten <- append(getBeadData(BLData, what = what, array = arraynms[1])[sel1],
+ getBeadData(BLData, what = what, array = arraynms[2])[sel2])
+ if(log) finten <- log2(finten)
+ nasinf <- !is.finite(finten) | is.na(finten)
+ finten <- finten[!nasinf]
+ }else{
+ stop("You can only specify 1 or 2 images per array")
+ }
+ if(is.null(probes)) probes <- sort(unique(pr))
+ probes <- probes[probes > 0 & !is.na(probes)]
+ noprobes <- length(probes)
+ pr <- pr[!nasinf]
+ if (imagesPerArray == 1) {
+ G <- GBeadStDev <- GNoBeads <- matrix(0, nrow = noprobes, ncol = len)
+ colnames(G) <- colnames(GBeadStDev) <- colnames(GNoBeads) <- arraynms
+ if (BLData at arrayInfo$channels == "two" && !is.null(BLData[[arraynms[1]]]$R) && whatelse == "R")
+ R <- RBeadStDev <- RNoBeads <- G
+ else R <- NULL
+ }
+ else if (imagesPerArray == 2) {
+ G <- GBeadStDev <- GNoBeads <- matrix(0, nrow = noprobes, ncol = (len/2))
+ colnames(G) <- colnames(GBeadStDev) <- colnames(GNoBeads) <- arraynms[seq(1, len, by = 2)]
+ if (BLData at arrayInfo$channels == "two" && !is.null(BLData[[arraynms[1]]]$R) && whatelse == "R")
+ R <- RBeadStDev <- RNoBeads <- G
+ else R <- NULL
+ }
+ i <- j <- 1
+ while (j <= len) {
+ probeIDs <- as.integer(pr)
+ start <- 0
+ blah <- rmxBeadSummary(x = finten, probeIDs = probeIDs, probes = probes,
+ eps = eps, eps.lower = eps.lower, eps.upper = eps.upper,
+ steps = steps, fsCor = fsCor, mad0 = mad0)
+ G[, i] <- blah$fore
+ GBeadStDev[, i] <- blah$sd
+ GNoBeads[, i] <- blah$noBeads
+ if (BLData at arrayInfo$channels == "two" && !is.null(BLData[[arraynms[i]]]$R) && whatelse == "R") {
+ if (imagesPerArray == 1) {
+ finten <- getBeadData(BLData, what = whatelse, array = arraynms[i])[sel]
+ if(log) finten <- log2(finten)
+ nasinf <- !is.finite(finten) | is.na(finten)
+ finten <- finten[!nasinf]
+ }
+ else if (imagesPerArray == 2) {
+ finten <- append(getBeadData(BLData, what = whatelse, array = arraynms[j])[sel1],
+ getBeadData(BLData, what = whatelse, array = arraynms[j + 1])[sel2])
+ if(log) finten <- log2(finten)
+ nasinf <- !is.finite(finten) | is.na(finten)
+ finten <- finten[!nasinf]
+ }
+ blah <- rmxBeadSummary(x = finten, probeIDs = probeIDs, probes = probes,
+ eps = eps, eps.lower = eps.lower, eps.upper = eps.upper,
+ steps = steps, fsCor = fsCor, mad0 = mad0)
+ R[, i] <- blah$fore
+ RBeadStDev[, i] <- blah$sd
+ RNoBeads[, i] <- blah$noBeads
+ }
+ j <- j + imagesPerArray
+ i <- i + 1
+ rm(probeIDs, blah)
+ gc()
+ if ((imagesPerArray == 1) && (i <= len)) {
+ sel <- getBeadData(BLData, what = "ProbeID", array = arraynms[i]) != 0
+ pr <- getBeadData(BLData, what = "ProbeID", array = arraynms[i])[sel]
+ finten <- getBeadData(BLData, what = what, array = arraynms[i])[sel]
+ if(log) finten <- log2(finten)
+ nasinf <- !is.finite(finten) | is.na(finten)
+ pr <- pr[!nasinf]
+ finten <- finten[!nasinf]
+ }
+ else if ((imagesPerArray == 2) && (j < len)) {
+ sel1 <- getBeadData(BLData, what = "ProbeID", array = arraynms[j]) != 0
+ sel2 <- getBeadData(BLData, what = "ProbeID", array = arraynms[j + 1]) != 0
+ pr <- append(getBeadData(BLData, what = "ProbeID", array = arraynms[j])[sel1],
+ getBeadData(BLData, what = "ProbeID", array = arraynms[j + 1])[sel2])
+ finten <- append(getBeadData(BLData, what = what, array = arraynms[j])[sel1],
+ getBeadData(BLData, what = what, array = arraynms[j + 1])[sel2])
+ if(log) finten <- log2(finten)
+ nasinf <- !is.finite(finten) | is.na(finten)
+ pr <- pr[!nasinf]
+ finten <- finten[!nasinf]
+ }
+ }
+ GBeadStDev <- GBeadStDev/sqrt(GNoBeads)
+ if(!is.null(R)) RBeadStDev <- RBeadStDev/sqrt(RNoBeads)
+ if (whatelse == "R") {
+ rownames(G) <- rownames(R) <- rownames(GBeadStDev) <- rownames(RBeadStDev) <- rownames(GNoBeads) <- rownames(RNoBeads) <- probes
+ BSData <- new("NChannelSet", R = R, G = G, GBeadStDev = GBeadStDev,
+ RBeadStDev = RBeadStDev, GNoBeads = GNoBeads, RNoBeads = RNoBeads)
+ }
+ else {
+ BSData <- new("ExpressionSetIllumina")
+ assayData(BSData) <- assayDataNew(exprs = G, se.exprs = GBeadStDev,
+ nObservations = GNoBeads, storage.mode = "list")
+ rownames(exprs(BSData)) <- rownames(se.exprs(BSData)) <- rownames(nObservations(BSData)) <- probes
+ featureData(BSData) <- new("AnnotatedDataFrame", data = data.frame(ProbeID = probes, row.names = probes))
+ }
+ if (nrow(pData(BLData)) == len) {
+ if (imagesPerArray == 2)
+ BSData at phenoData <- new("AnnotatedDataFrame", data = pData(BLData at phenoData)[arrayord, , drop = FALSE][seq(1, len, by = 2), , drop = FALSE])
+ else BSData at phenoData <- BLData at phenoData
+ }
+ else {
+ BSData at phenoData <- new("AnnotatedDataFrame", data = data.frame(sampleName = colnames(G)))
+ }
+ if (!is.null(pData(BSData)$sampleName))
+ sampleNames(BSData) <- pData(BSData)$sampleName
+ else sampleNames(BSData) <- colnames(G)
+ if (whatelse == "R") {
+ varMetadata <- data.frame(labelDescription = colnames(BSData at phenoData@data), channel = "_ALL_")
+ BSData at phenoData <- new("AnnotatedDataFrame", data = data.frame(BSData at phenoData@data), varMetadata = varMetadata)
+ }
+ BSData at annotation <- BLData at annotation
+ if ("qcScores" %in% names(BLData at arrayInfo))
+ t <- try(BSData at BeadLevelQC <- BLData at arrayInfo$qcScores, silent = TRUE)
+ BSData
+ })
+## computation of bead summaries via robloxbioc for "matrix"
+rmxBeadSummary <- function(x, probeIDs, probes, eps, eps.lower, eps.upper, steps, fsCor, mad0){
+ comIDs <- intersect(probeIDs, probes)
+ x <- x[probeIDs %in% comIDs]
+ probeIDs <- probeIDs[probeIDs %in% comIDs]
+ noBeads <- as.vector(table(probeIDs))
+ noBeads.uni <- as.integer(names(table(noBeads)))
+ probes1 <- comIDs
+ len1 <- length(probes1)
+ fore1 <- numeric(len1)
+ SD1 <- numeric(len1)
+ for(i in seq(along = noBeads.uni)){
+ index <- noBeads == noBeads.uni[i]
+ IDs <- probes1[index]
+ if(noBeads.uni[i] == 1){
+ fore1[index] <- x[probeIDs %in% IDs]
+ SD1[index] <- mad0
+ }else{
+ temp <- matrix(x[probeIDs %in% IDs], ncol = noBeads.uni[i], byrow = TRUE)
+ rmx <- robloxbioc(temp, eps = eps, eps.lower = eps.lower, eps.upper = eps.upper,
+ steps = steps, fsCor = fsCor, mad0 = mad0)
+ fore1[index] <- rmx[,"mean"]
+ SD1[index] <- rmx[,"sd"]
+ }
+ }
+ len <- length(probes)
+ fore <- numeric(len)
+ SD <- numeric(len)
+ noBeads1 <- numeric(len)
+ nas <- !(probes %in% comIDs)
+ fore[nas] <- NA
+ fore[!nas] <- fore1
+ SD[nas] <- NA
+ SD[!nas] <- SD1
+ noBeads1[nas] <- 0
+ noBeads1[!nas] <- noBeads
+
+ return(list(fore = fore, sd = SD, noBeads = noBeads1))
+}
Deleted: pkg/RobLoxBioC/R/robloxbiocBeadLevelList.R
===================================================================
--- pkg/RobLoxBioC/R/robloxbiocBeadLevelList.R 2012-03-03 22:18:35 UTC (rev 463)
+++ pkg/RobLoxBioC/R/robloxbiocBeadLevelList.R 2012-03-03 22:30:52 UTC (rev 464)
@@ -1,202 +0,0 @@
-setMethod("robloxbioc", signature(x = "BeadLevelList"),
- function(x, log = TRUE, imagesPerArray = 1, what = "G", probes = NULL, arrays = NULL,
- eps = NULL, eps.lower = 0, eps.upper = 0.05, steps = 3L,
- fsCor = TRUE, mad0 = 1e-4){
- BLData <- x
- arraynms <- sectionNames(BLData)
- if(!is.null(arrays) && !is.character(arrays)) arraynms <- arraynms[arrays]
- if(is.character(arrays)) arraynms <- which(arraynms %in% arrays)
- len <- length(arraynms)
- what <- match.arg(what, c("G", "R", "RG", "M", "A", "beta"))
- whatelse <- ""
- if(what == "RG"){
- if(BLData at arrayInfo$channels == "two"){
- what <- "G"
- whatelse <- "R"
- }else{
- stop("Need two-channel data to calculate summary R and G values")
- }
- }
- if(imagesPerArray == 1){
- pr <- getBeadData(BLData, what = "ProbeID", array = arraynms[1])
- sel <- pr != 0
- pr <- pr[sel]
- finten <- getBeadData(BLData, what = what, array = arraynms[1])[sel]
- if(log) finten <- log2(finten)
- nasinf <- !is.finite(finten) | is.na(finten)
- finten <- finten[!nasinf]
- }
- else if(imagesPerArray == 2){
- if(length(arraynms)%%2 != 0)
- stop("Need an even number of arrays when 'imagesPerArray=2'")
- arrayord <- order(arraynms)
- arraynms <- arraynms[arrayord]
- tmp <- unlist(strsplit(arraynms, "_"))
- chipnums <- tmp[seq(1, length(tmp), by = 3)]
- pos <- tmp[seq(2, length(tmp), by = 3)]
- stripnum <- as.numeric(tmp[seq(3, length(tmp), by = 3)])
- check <- ((chipnums[seq(1, len, by = 2)] == chipnums[seq(2, len, by = 2)])
- & (pos[seq(1, len, by = 2)] == pos[seq(2, len, by = 2)])
- & (stripnum[seq(1, len, by = 2)] == stripnum[seq(2, len, by = 2)] - 1))
- if (sum(check) != length(check))
- stop("Missing arrays")
- sel1 <- getBeadData(BLData, what = "ProbeID", array = arraynms[1]) != 0
- sel2 <- getBeadData(BLData, what = "ProbeID", array = arraynms[2]) != 0
- pr <- append(getBeadData(BLData, what = "ProbeID", array = arraynms[1])[sel1],
- getBeadData(BLData, what = "ProbeID", array = arraynms[2])[sel2])
- finten <- append(getBeadData(BLData, what = what, array = arraynms[1])[sel1],
- getBeadData(BLData, what = what, array = arraynms[2])[sel2])
- if(log) finten <- log2(finten)
- nasinf <- !is.finite(finten) | is.na(finten)
- finten <- finten[!nasinf]
- }else{
- stop("You can only specify 1 or 2 images per array")
- }
- if(is.null(probes)) probes <- sort(unique(pr))
- probes <- probes[probes > 0 & !is.na(probes)]
- noprobes <- length(probes)
- pr <- pr[!nasinf]
- if (imagesPerArray == 1) {
- G <- GBeadStDev <- GNoBeads <- matrix(0, nrow = noprobes, ncol = len)
- colnames(G) <- colnames(GBeadStDev) <- colnames(GNoBeads) <- arraynms
- if (BLData at arrayInfo$channels == "two" && !is.null(BLData[[arraynms[1]]]$R) && whatelse == "R")
- R <- RBeadStDev <- RNoBeads <- G
- else R <- NULL
- }
- else if (imagesPerArray == 2) {
- G <- GBeadStDev <- GNoBeads <- matrix(0, nrow = noprobes, ncol = (len/2))
- colnames(G) <- colnames(GBeadStDev) <- colnames(GNoBeads) <- arraynms[seq(1, len, by = 2)]
- if (BLData at arrayInfo$channels == "two" && !is.null(BLData[[arraynms[1]]]$R) && whatelse == "R")
- R <- RBeadStDev <- RNoBeads <- G
- else R <- NULL
- }
- i <- j <- 1
- while (j <= len) {
- probeIDs <- as.integer(pr)
- start <- 0
- blah <- rmxBeadSummary(x = finten, probeIDs = probeIDs, probes = probes,
- eps = eps, eps.lower = eps.lower, eps.upper = eps.upper,
- steps = steps, fsCor = fsCor, mad0 = mad0)
- G[, i] <- blah$fore
- GBeadStDev[, i] <- blah$sd
- GNoBeads[, i] <- blah$noBeads
- if (BLData at arrayInfo$channels == "two" && !is.null(BLData[[arraynms[i]]]$R) && whatelse == "R") {
- if (imagesPerArray == 1) {
- finten <- getBeadData(BLData, what = whatelse, array = arraynms[i])[sel]
- if(log) finten <- log2(finten)
- nasinf <- !is.finite(finten) | is.na(finten)
- finten <- finten[!nasinf]
- }
- else if (imagesPerArray == 2) {
- finten <- append(getBeadData(BLData, what = whatelse, array = arraynms[j])[sel1],
- getBeadData(BLData, what = whatelse, array = arraynms[j + 1])[sel2])
- if(log) finten <- log2(finten)
- nasinf <- !is.finite(finten) | is.na(finten)
- finten <- finten[!nasinf]
- }
- blah <- rmxBeadSummary(x = finten, probeIDs = probeIDs, probes = probes,
- eps = eps, eps.lower = eps.lower, eps.upper = eps.upper,
- steps = steps, fsCor = fsCor, mad0 = mad0)
- R[, i] <- blah$fore
- RBeadStDev[, i] <- blah$sd
- RNoBeads[, i] <- blah$noBeads
- }
- j <- j + imagesPerArray
- i <- i + 1
- rm(probeIDs, blah)
- gc()
- if ((imagesPerArray == 1) && (i <= len)) {
- sel <- getBeadData(BLData, what = "ProbeID", array = arraynms[i]) != 0
- pr <- getBeadData(BLData, what = "ProbeID", array = arraynms[i])[sel]
- finten <- getBeadData(BLData, what = what, array = arraynms[i])[sel]
- if(log) finten <- log2(finten)
- nasinf <- !is.finite(finten) | is.na(finten)
- pr <- pr[!nasinf]
- finten <- finten[!nasinf]
- }
- else if ((imagesPerArray == 2) && (j < len)) {
- sel1 <- getBeadData(BLData, what = "ProbeID", array = arraynms[j]) != 0
- sel2 <- getBeadData(BLData, what = "ProbeID", array = arraynms[j + 1]) != 0
- pr <- append(getBeadData(BLData, what = "ProbeID", array = arraynms[j])[sel1],
- getBeadData(BLData, what = "ProbeID", array = arraynms[j + 1])[sel2])
- finten <- append(getBeadData(BLData, what = what, array = arraynms[j])[sel1],
- getBeadData(BLData, what = what, array = arraynms[j + 1])[sel2])
- if(log) finten <- log2(finten)
- nasinf <- !is.finite(finten) | is.na(finten)
- pr <- pr[!nasinf]
- finten <- finten[!nasinf]
- }
- }
- GBeadStDev <- GBeadStDev/sqrt(GNoBeads)
- if(!is.null(R)) RBeadStDev <- RBeadStDev/sqrt(RNoBeads)
- if (whatelse == "R") {
- rownames(G) <- rownames(R) <- rownames(GBeadStDev) <- rownames(RBeadStDev) <- rownames(GNoBeads) <- rownames(RNoBeads) <- probes
- BSData <- new("NChannelSet", R = R, G = G, GBeadStDev = GBeadStDev,
- RBeadStDev = RBeadStDev, GNoBeads = GNoBeads, RNoBeads = RNoBeads)
- }
- else {
- BSData <- new("ExpressionSetIllumina")
- assayData(BSData) <- assayDataNew(exprs = G, se.exprs = GBeadStDev,
- nObservations = GNoBeads, storage.mode = "list")
- rownames(exprs(BSData)) <- rownames(se.exprs(BSData)) <- rownames(nObservations(BSData)) <- probes
- featureData(BSData) <- new("AnnotatedDataFrame", data = data.frame(ProbeID = probes, row.names = probes))
- }
- if (nrow(pData(BLData)) == len) {
- if (imagesPerArray == 2)
- BSData at phenoData <- new("AnnotatedDataFrame", data = pData(BLData at phenoData)[arrayord, , drop = FALSE][seq(1, len, by = 2), , drop = FALSE])
- else BSData at phenoData <- BLData at phenoData
- }
- else {
- BSData at phenoData <- new("AnnotatedDataFrame", data = data.frame(sampleName = colnames(G)))
- }
- if (!is.null(pData(BSData)$sampleName))
- sampleNames(BSData) <- pData(BSData)$sampleName
- else sampleNames(BSData) <- colnames(G)
- if (whatelse == "R") {
- varMetadata <- data.frame(labelDescription = colnames(BSData at phenoData@data), channel = "_ALL_")
- BSData at phenoData <- new("AnnotatedDataFrame", data = data.frame(BSData at phenoData@data), varMetadata = varMetadata)
- }
- BSData at annotation <- BLData at annotation
- if ("qcScores" %in% names(BLData at arrayInfo))
- t <- try(BSData at BeadLevelQC <- BLData at arrayInfo$qcScores, silent = TRUE)
- BSData
- })
-## computation of bead summaries via robloxbioc for "matrix"
-rmxBeadSummary <- function(x, probeIDs, probes, eps, eps.lower, eps.upper, steps, fsCor, mad0){
- comIDs <- intersect(probeIDs, probes)
- x <- x[probeIDs %in% comIDs]
- probeIDs <- probeIDs[probeIDs %in% comIDs]
- noBeads <- as.vector(table(probeIDs))
- noBeads.uni <- as.integer(names(table(noBeads)))
- probes1 <- comIDs
- len1 <- length(probes1)
- fore1 <- numeric(len1)
- SD1 <- numeric(len1)
- for(i in seq(along = noBeads.uni)){
- index <- noBeads == noBeads.uni[i]
- IDs <- probes1[index]
- if(noBeads.uni[i] == 1){
- fore1[index] <- x[probeIDs %in% IDs]
- SD1[index] <- mad0
- }else{
- temp <- matrix(x[probeIDs %in% IDs], ncol = noBeads.uni[i], byrow = TRUE)
- rmx <- robloxbioc(temp, eps = eps, eps.lower = eps.lower, eps.upper = eps.upper,
- steps = steps, fsCor = fsCor, mad0 = mad0)
- fore1[index] <- rmx[,"mean"]
- SD1[index] <- rmx[,"sd"]
- }
- }
- len <- length(probes)
- fore <- numeric(len)
- SD <- numeric(len)
- noBeads1 <- numeric(len)
- nas <- !(probes %in% comIDs)
- fore[nas] <- NA
- fore[!nas] <- fore1
- SD[nas] <- NA
- SD[!nas] <- SD1
- noBeads1[nas] <- 0
- noBeads1[!nas] <- noBeads
-
- return(list(fore = fore, sd = SD, noBeads = noBeads1))
-}
Modified: pkg/RobLoxBioC/man/robloxbioc.Rd
===================================================================
--- pkg/RobLoxBioC/man/robloxbioc.Rd 2012-03-03 22:18:35 UTC (rev 463)
+++ pkg/RobLoxBioC/man/robloxbioc.Rd 2012-03-03 22:30:52 UTC (rev 464)
@@ -3,7 +3,7 @@
\alias{robloxbioc-methods}
\alias{robloxbioc,matrix-method}
\alias{robloxbioc,AffyBatch-method}
-\alias{robloxbioc,BeadLevelList-method}
+\alias{robloxbioc,BeadLevelData-method}
\title{Generic Function for Preprocessing Biological Data}
\description{
@@ -22,7 +22,7 @@
mad0 = 1e-4, contrast.tau = 0.03, scale.tau = 10,
delta = 2^(-20), sc = 500)
-\S4method{robloxbioc}{BeadLevelList}(x, log = TRUE, imagesPerArray = 1, what = "G", probes = NULL,
+\S4method{robloxbioc}{BeadLevelData}(x, log = TRUE, imagesPerArray = 1, what = "G", probes = NULL,
arrays = NULL, eps = NULL, eps.lower = 0, eps.upper = 0.05,
steps = 3L, fsCor = TRUE, mad0 = 1e-4)
}
@@ -60,7 +60,7 @@
Normally 1 for a SAM and 1 or 2 for a BeadChip. The images (strips) from the same array
will be combined so that each column in the output represents a sample. }
\item{what}{ character string specifying which intensities/values to summarize.
- See \code{\link[beadarray]{getArrayData}} for a list of possibilities. }
+ See \code{\link[beadarray]{getBeadData}} for a list of possibilities. }
\item{probes}{ Specify particular probes to summarize. If left \code{NULL} then all
the probes on the first array are used. }
\item{arrays}{ integer (scalar or vector) specifying the strips/arrays to summarize.
@@ -100,6 +100,7 @@
\value{ Return value depends on the class of \code{x}.
In case of \code{"matrix"} a matrix with columns "mean" and "sd" is returned.
In case of \code{"AffyBatch"} an object of class \code{"ExpressionSet"} is returned.
+ In case of \code{"BeadLevelData"} an object of class \code{"ExpressionSetIllumina"} is returned.
}
\references{
Affymetrix, Inc. (2002). \emph{Statistical Algorithms Description Document}.
@@ -168,13 +169,12 @@
## using Illumina-Data
\dontrun{
## "Not run" just because of computation time
-if(require(beadarrayExampleData)){
- data(exampleBLData)
- res <- robloxbioc(exampleBLData, eps.upper = 0.5)
- res
+require(beadarrayExampleData)
+data(exampleBLData)
+res <- robloxbioc(exampleBLData, eps.upper = 0.5)
+res
}
}
-}
\concept{normal location and scale}
\concept{infinitesimal robustness}
\concept{radius-minimax estimator}
More information about the Robast-commits
mailing list