## ----knitr, echo=FALSE, results="hide"----------------------------------- library("knitr") opts_chunk$set(tidy=FALSE,dev="png",fig.show="as.is", fig.width=10,fig.height=6, message=FALSE,eval=T,warning=FALSE) ## ----style, eval=TRUE, echo=F, results="asis"---------------------------- BiocStyle::latex() ## ----prelim, echo=TRUE--------------------------------------------------- library(beadarrayExampleData) library(beadarray) data(exampleBLData) ## ----options, echo=FALSE, eval=TRUE-------------------------------------- options(width = 80) ## ----readIllumina, echo=TRUE, eval=FALSE--------------------------------- ## BLData = readIllumina(useImages=FALSE, illuminaAnnotation = "Humanv3") ## ----annotation---------------------------------------------------------- suggestAnnotation(exampleBLData,verbose=TRUE) annotation(exampleBLData) <-"Humanv3" ## ----BLData-------------------------------------------------------------- class(exampleBLData) slotNames(exampleBLData) ##Get the beadData for array-section 1 exampleBLData[[1]][1:10,] ##Alternative using accessor function getBeadData(exampleBLData, array=1, what="Grn")[1:10] ##Get unique ProbeIDs. These are the ArrayAddressIDs uIDs = unique(getBeadData(exampleBLData, array=1, what="ProbeID")) uIDs[1:10] ## ----metrics------------------------------------------------------------- metrics(exampleBLData) p95(exampleBLData, "Grn") snr(exampleBLData, "Grn") ## ----transform----------------------------------------------------------- log2(exampleBLData[[1]][1:10,2]) logGreenChannelTransform logGreenChannelTransform(exampleBLData, array=1)[1:10] logRedChannelTransform ## ----Imageplot1---------------------------------------------------------- imageplot(exampleBLData, array=1, low="lightgreen", high="darkgreen") ## ----Imageplot2---------------------------------------------------------- imageplot(exampleBLData, array=2, low="lightgreen", high="darkgreen") ## ----BASH, eval=FALSE---------------------------------------------------- ## ## ## bsh = BASH(exampleBLData, array=1:2) ## ## ----savingBASH, eval=FALSE---------------------------------------------- ## ## for(i in 1:2){ ## ## BLData <- setWeights(exampleBLData, wts=bsh$wts[[i]], array=i) ## ## } ## ## BLData <- insertSectionData(exampleBLData, what="BASHQC", data = bsh$QC) ## ## ----getBASH------------------------------------------------------------- table(getBeadData(exampleBLData, array=1, what="wts")) table(getBeadData(exampleBLData, array=2, what="wts")) ## ----masks--------------------------------------------------------------- showArrayMask(exampleBLData, array=2) ## ----controlPlot--------------------------------------------------------- p <- combinedControlPlot(exampleBLData) ## ----doPlot, echo=FALSE-------------------------------------------------- if(!is.null(p)){ p } else plot(1:10,type="n",axes=F, ) ## ----createBeadSummaryData----------------------------------------------- BSData <- summarize(exampleBLData) ## ----createBeadSummaryData2, echo=TRUE,eval=FALSE------------------------ ## ## myMedian <- function(x) median(x, na.rm=TRUE) ## myMad <- function(x) mad(x, na.rm=TRUE) ## ## greenChannel2 <- new("illuminaChannel", greenChannelTransform, illuminaOutlierMethod, ## myMedian, myMad,"G") ## ## BSData2 <- summarize(exampleBLData, list(greenChannel2)) ## ## ----showBSData, echo=TRUE----------------------------------------------- BSData ## ----calculateDetection, echo=TRUE--------------------------------------- det = calculateDetection(BSData) head(det) Detection(BSData) <- det ## ----sessionInfo--------------------------------------------------------- sessionInfo()