## ----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() ## ----options, echo=FALSE, eval=TRUE-------------------------------------- options(width = 70) ## ----prelim, echo=FALSE, eval=TRUE--------------------------------------- library(beadarray) ## ----readingTiff, eval=FALSE--------------------------------------------- ## tiff <- readTIFF(); ## data <- readBeadLevelTextFile(); ## ----standardProcessing, eval=FALSE-------------------------------------- ## bg <- illuminaBackground(tiff, data[,3:4]); ## tiffSharp <- illuminaSharpen(tiff); ## fg <- illuminaForeground(tiffSharp, data[,3:4]); ## finalIntensity <- fg - bg; ## ----creatingObject, eval=FALSE------------------------------------------ ## BLData <- new(Class = "beadLevelData"); ## BLData <- insertBeadData(BLData, array = 1, what = "Grn", data = finalIntensity) ## ----usingReadIllumina, eval=FALSE--------------------------------------- ## BLData <- readIllumina(); ## BLData <- insertBeadData(BLData, array = 1, what = "Grn", data = finalIntensity) ## BLData <- insertBeadData(BLData, array = 1, what = "GrnLog", data = log2(finalIntensity)) ## ----alternativeMethods, eval=FALSE-------------------------------------- ## bg <- medianBackground(tiff, data[,3:4]); ## ----sessionInfo--------------------------------------------------------- sessionInfo()