### R code from vignette source 'beadarrayExampleData.Rnw' ################################################### ### code chunk number 1: beadarrayExampleData.Rnw:30-31 ################################################### options(width=70) ################################################### ### code chunk number 2: beadarrayExampleData.Rnw:43-50 ################################################### library(beadarrayExampleData) data(exampleBLData) exampleBLData data(exampleSummaryData) exampleSummaryData pData(exampleSummaryData) ################################################### ### code chunk number 3: beadarrayExampleData.Rnw:58-86 (eval = FALSE) ################################################### ## ## require(BeadArrayUseCases) ## ## targets <- read.table(system.file("extdata/BeadLevelBabFiles/targetsHT12.txt", package = "BeadArrayUseCases"), header=TRUE, sep="\t", as.is=TRUE) ## sn <- paste(targets[,3], targets[,4], sep="_") ## ## babFilePath <- system.file("extdata/BeadLevelBabFiles", package = "BeadArrayUseCases") ## ## exampleBLData <- readIllumina(dir=babFilePath, sectionNames=sn[c(1,12)], useImages=FALSE, illuminaAnnotation="Humanv3") ## ## bsh <- BASH(exampleBLData,array=c(1,2)) ## ## exampleBLData <- setWeights(exampleBLData, wts = bsh$wts, array=1:2) ## ## data <- readIllumina(dir=babFilePath, sectionNames=sn, useImages=FALSE, illuminaAnnotation="Humanv3") ## ## ## grnchannel <- new("illuminaChannel", transFun = logGreenChannelTransform, outlierFun = illuminaOutlierMethod, exprFun = function(x) mean(x,na.rm=TRUE), varFun= function(x) sd(x, na.rm=TRUE),channelName= "G") ## ## ## grnchannel.unlogged <- new("illuminaChannel", transFun = greenChannelTransform, outlierFun = illuminaOutlierMethod, exprFun = function(x) mean(x,na.rm=TRUE), varFun= function(x) sd(x, na.rm=TRUE),channelName= "G.ul") ## ## exampleSummaryData <- summarize(data, list(grnchannel, grnchannel.unlogged), useSampleFac=FALSE) ## ## ## pData(exampleSummaryData)[,2] <- targets[,2] ## ##