processArrayDataObject {arrayMagic}R Documentation

Automated processing and normalisation of an arrayData-object (part of function processArrayData)

Description

Automated processing and normalisation of an arrayData-object. The function is called by processArrayData.

Usage

processArrayDataObject(arrayDataObject, spotIdentifier = "Name", verbose = TRUE, normalisationMethod = "vsn", subtractBackground=FALSE, spotsRemovedBeforeNormalisation = NULL, spotsRemovedAfterNormalisation = NULL, subGroups = NULL, channelsSeparately = FALSE, hybridisationGroups = NULL)

Arguments

arrayDataObject object of class arrayData-class; required; default missing
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
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

Value

A list of objects, i.e. an "exprSetRGObject" and "arrayDataObject" with corresponding class types exprSetRG-class, arrayData-class.

Author(s)

Andreas Buness <a.buness@dkfz.de>

See Also

processArrayData, normalise, exprSetRG-class, arrayData-class

Examples

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

       slideDescription <- readpDataSlides(
                             loadPath=LOADPATH, 
                             slideDescriptionFile=SLIDEDESCRIPTIONFILE
                           )
        arrayDataObject <- readIntensities(
                             loadPath=LOADPATH,
                             slideDescription=slideDescription
                          )

       resultList <- processArrayDataObject( arrayDataObject=arrayDataObject )
         
 

[Package arrayMagic version 1.16.1 Index]