processArrayData {arrayMagic} | R Documentation

## Automated processing of two colour DNA microarray data

### Description

Automated processing of image analyis result files and related annotation information. Combines several steps of microarray data processing, read the package vignette for a detailed example. To access the vignette call openVignette() after calling library(arrayMagic).

### Usage

    processArrayData(spotIdentifier = "Name", verbose = TRUE, loadPath = ".", slideDescriptionFile = "slideDescription.txt", deleteBlanks = TRUE, normalisationMethod = "vsn", subtractBackground=FALSE, spotsRemovedBeforeNormalisation = NULL, spotsRemovedAfterNormalisation = NULL, subGroups = NULL, channelsSeparately = FALSE, hybridisationGroups = NULL, savePath = ".", objectsFileName, plotOutput = "screen", fileNameColumn = "fileName", slideNameColumn, type = "GenePix", dataColumns = NULL, spotAnnoColumns = NULL, channelColumn = NULL, removePatterns = NULL, skip = NULL, ...)

### Arguments

`spotIdentifier` | character string; required; default "Name". `spotIdentifier` specifies the column in the image analysis result files which contain spot or gene identifiers
`verbose` | logical; required; default: `TRUE`
`loadPath` | character string; required; default: ".". The path is used for loading of the `slideDescriptionFile` and the image analysis result files; note: "." refers to the working directory.
`slideDescriptionFile` | character string; required; default "slideDescription.txt". The first line of the tab-deliminated file must contain all column names, i.e. a header line. In particular it must contain the column named `fileNameColum` and possibly additionally a column named `slideNameColumn`.
`deleteBlanks` | logical; required; default: `TRUE`. If set to `TRUE` any blank character (space) is removed from the text body of the `slideDescriptionFile`.
`fileNameColumn` | character string; required; default: "fileName". `fileNameColumn` specifies the column which contains the names of all image analysis result files.
`slideNameColumn` | character string; optional; default missing. If `slideNameColumn` is missing the value is set to `fileNameColumn`.
`channelColumn` | optional; cf. `readIntensities`; default: `NULL`
`type` | character string to characterize the file type like "GenePix" or "generic"; note e.g. "generic" requires the arguments `dataColumns` and `spotAnnoColumns`; default: "GenePix"; cf. `readIntensities` for details
`dataColumns` | required for `type` "generic"; cf. `readIntensities`; default: `NULL`
`spotAnnoColumns` | required for `type` "generic"; cf. `readIntensities`; default: `NULL`
`removePatterns` | optional; cf. `readIntensities`; default: `NULL`
`skip` | optional; cf. `readIntensities`; default: `NULL`
`...` | further arguments which are passed to `readIntensities` and eventually are passed to `read.table`.
`normalisationMethod` | character string; required; default: "vsn"; cf. argument `method` of `normalise`
`subtractBackground` | logical; required; default: `FALSE` cf. `normalise`
`spotsRemovedBeforeNormalisation` | vector of character strings; required; default: `NULL`. All spots which match the string(s) will be excluded already before normalisation and will not be present in the resulting objects at all.
`spotsRemovedAfterNormalisation` | vector of character strings; required; default: `NULL`; cf. argument `spotsRemovedBeforeNormalisation`.
`subGroups` | character string or `NULL`; required; cf. `normalise`; default: `NULL`
`channelsSeparately` | logical; required; cf. `normalise`; default `FALSE`
`hybridisationGroups` | list of numeric vectors; cf. `normalise`; required; default: `NULL`
`savePath` | character string; required; default: ".". The directory `savePath` used to store the results (cf. argument `objectsFileName` and processed files. If the path does not exist a directory is created; note: "." refers to the working directory.
`objectsFileName` | character string; optional; default missing, i.e. no file is created. `objectsFileName` specifies the name of the file used to store the object "resultList", i.e. the return value of the function.
`plotOutput` | character string; required; default: "screen"; Possible values: "screen", "pdf" or "win.metafile".

### Value

A list of objects, i.e. an "exprSetRGObject" and an "arrayDataObject" with corresponding class types `exprSetRG-class` and `arrayData-class` (cf. the result of `processArrayDataObject`). Side-effects: The result list "resultList" is stored as file `objectsFileName` in the directory `savePath` if the argument `objectsFileName` is supplied. The `slideDescriptionFile` is stored with suffix "_processed" in the directory `savePath`.

### Author(s)

Andreas Buness <a.buness@dkfz.de>

### See Also

`readpDataSlides`, `readIntensities`, `processArrayDataObject`, `normalise`, `exprSetRG-class`, `arrayData-class`

### Examples

           LOADPATH <- file.path(.path.package("arrayMagic"), "extdata")
           SAVEPATH <- tempdir()
            SLIDEDESCRIPTIONFILE <- "slideDescription"

            resultList <- processArrayData(
                                 loadPath=LOADPATH,
                                  savePath=SAVEPATH,
                                 slideDescriptionFile=SLIDEDESCRIPTIONFILE
                      )
           writeToFile(arrayDataObject=resultList$arrayDataObject,
                       exprSetRGObject=resultList$exprSetRGObject,
                       fileName="normalisedData.txt",
                       savePath=SAVEPATH)

           summarizedResult <- slideMerge(exprSetRGObject=resultList$exprSetRGObject, slideMergeColumn="replicates" )

            qPL <- qualityParameters(arrayDataObject=resultList$arrayDataObject,
                                     exprSetRGObject=resultList$exprSetRGObject)

            visualiseQualityParameters(qualityParameters=qPL$qualityParameters,
                                       savePath=tempdir())

            qualityDiagnostics(
                        arrayDataObject=resultList$arrayDataObject,
                        exprSetRGObject=resultList$exprSetRGObject,
                        qualityParametersList=qPL,
                        groupingColumn="replicates",
                        slideNameColumn="fileName",
                        savePath=tempdir(),
                        plotOutput="pdf")

            unlink(file.path(SAVEPATH, paste(SLIDEDESCRIPTIONFILE,"_processed",sep="")))
             resultListG <- processArrayData(
                                 loadPath=LOADPATH,
                                  savePath=SAVEPATH,
                                 slideDescriptionFile=SLIDEDESCRIPTIONFILE,
                                 plotOutput="pdf",
                                 hybridisationGroups = list((1:4),(5:9))
                      )
     unlink(file.path(SAVEPATH, paste(SLIDEDESCRIPTIONFILE,"_processed",sep="")))
     resultListG2 <- processArrayData(
                                 loadPath=LOADPATH,
                                  savePath=SAVEPATH,
                                 slideDescriptionFile=SLIDEDESCRIPTIONFILE,
                                 plotOutput="pdf",
                                 objectsFileName = "exprSetRG.RData",
                                 hybridisationGroups = "slideBySlide"
                                             )
     unlink(file.path(SAVEPATH, paste(SLIDEDESCRIPTIONFILE,"_processed",sep="")))

     SLIDEDESCRIPTIONFILE <- "genericChannelsPerFile"
     spotAnnoColumns <- c("Index", "Label" , "Type" , "Name" , "ID" )
     dataColumns <- c("Normalized....","Average....","Normalized....","Average....")
     names(dataColumns) <- c("greenForeground","greenBackground",
                          "redForeground","redBackground")

     resultGenericChannel <- processArrayData(
                                    spotIdentifier="Index",
                                    loadPath=LOADPATH,
                                    savePath=SAVEPATH,
                                    slideDescriptionFile=SLIDEDESCRIPTIONFILE,
                                    normalisationMethod="none",
                                    channelColumn="channel",
                                    fileNameColumn="files",
                                    slideNameColumn="name",
                                    type="genericOneFilePerChannel",
                                    spotAnnoColumns=spotAnnoColumns,
                                    dataColumns=dataColumns
                                )

     unlink(file.path(SAVEPATH, paste(SLIDEDESCRIPTIONFILE,"_processed",sep="")))
     SLIDEDESCRIPTIONFILE <- "genericChannelsPerFileTwo"
     dataColumns <- c("Integral..QL.","Bkg..QL.", "Integral..QL.","Bkg..QL.")
     names(dataColumns) <- c("greenForeground","greenBackground",
                          "redForeground","redBackground")

     resultGenericChannelTwo <- processArrayData(
                                    spotIdentifier="ID",
                                    loadPath=LOADPATH,
                                    savePath=SAVEPATH,
                                    slideDescriptionFile=SLIDEDESCRIPTIONFILE,
                                    normalisationMethod="vsn",
                                    channelColumn="channel",
                                    fileNameColumn="files",
                                    slideNameColumn="name",
                                    subtractBackground=TRUE,
                                    type="genericOneFilePerChannel",
                                    spotAnnoColumns=spotAnnoColumns,
                                    dataColumns=dataColumns
                                )
     unlink(file.path(SAVEPATH, paste(SLIDEDESCRIPTIONFILE,"_processed",sep="")))

[Package arrayMagic version 1.12.2 Index]